And I don't want to offend anyone (control or synthesis fans) but I think (my opinion only) both options are just wrong and don't fit the story of the whole trilogy at all it doesn't have anything to do with being renegade or not
To clarify when I mentioned renegade I didn't necessarily mean it due to the moral alignment but rather due to the dialogue it delivers. The paragon response in that conversation has Shepard criticizing TIM for playing with powers we "shouldn't be allowed to have" - to paraphrase. The paragon responses do lend towards Shepard having a moral and/or ethical disagreement with controlling the reapers. The renegade response however does not have such an anti-control bias. The renegade Shepard even encourages it, saying, again paraphrasing, "if you can control the reapers then what are you waiting for it, do it and end this war! You can't, can you? Because they're controlling you!"
Essentially the paragon dialogue does seem to be against the mere concept of control which would make Shepard choosing control seem rather hypocritical. The renegade line of dialogue however doesn't have Shepard saying control is 'wrong'. Renegade Shep's argument is more against TIM specifically and not his ideology in regards to controlling the reapers. So for renegade Shep to choose control it wouldn't necessarily come across as being hypocritical. That was what I was trying to say, anyway. I'm not arguing that there isn't potential for hypocritical behavior on Shepard's part, just that it isn't NECESSARY since Shepard's stance on that is up to the player and not really set-in-stone, as it were.
the catalyst like you suggested he shouldn't have existed his logic is crazy but what I hate even more is that the whole synthetics vs organics subplot which was perfectly resolved on Rannoch (one way or the other) gets dragged into the reapers storyline
You keep bringing up his logic. I agree that the catalyst shouldn't have existed. Mainly because I feel its existence contradicts a lot of the reaper lore up until that point, or at least it does in the form it is presented. I also feel like it contradicts the purpose of the first game. However, as I mentioned before, I have no issue with its actual logic. Its explained in the story quite a bit and fits in well with the trilogy as a whole. What specifically about it do you take offense to enough to hate it from a narrative perspective?
As for the synthetic vs organic plot... I understand why you might think this is resolved with the geth but I put forth that you should think much bigger than that. The reapers are a multi-billion year old species. Think about that for a moment. That's really old. Really, really old. Hell, they potentially could be older than the Earth itself. The claim the starbrat makes is rather broad. It says that the peace between organic and synthetic will not last. In YOUR lifetime it might indeed last. In your kids lifetime, in your grandkids... it may last for a very long time in relation to our pitiful lifespan. Consider it from the perspective of an immortal, multi-billion year old species. The peace WON'T last. It's impossible to last.
Conflict is the rule of the cosmos, much like Javik told us in our conversations with him. The alternative is that peace between synthetic and organic lasts for all eternity. A preposterous claim! The starbrat's claim is so broad that it cannot be wrong. Also remember the pattern exists in the mass effect universe. The multi-billion year old species of Leviathan, the intelligence, the reapers and even the protheans (though not as old themselves, obviously) have all told us in the game multiple times that this cycle exists. It's an observable fact in the Mass Effect universe. The reality of this fact is not diminished because Shepard potentially brokered a peace with the geth for a few weeks.
This conclusion of a synthetic vs organic cycle comes from the perspective of beings that have been observing the pattern for billions of years. Can you fathom how long that is? In the Mass Effect lore this is a reoccurring pattern that has always persisted. It is possible, not plausible, that in the existence of our species peace with synthetics will last... Huge stretch but possible. It is not however possible for it to last for all eternity. The leviathans and reapers are essentially immortal beings. It does not matter how long the peace lasts relative to us, the pattern is there regardless even if you have to wait millions of years to observe it. This multi-billion year old perspective is not magically made invalid due to a few weeks of sustained peace with the geth.
Just try to picture this on a very BIG picture scale, from the perspective of a being that is immortal. Nothing Shepard has done invalidates the cycle. I would even go as far as to say it is naive to think it does.
Furthermore this twist of synthetic vs organic is nothing new in the series. Sure, its new in relation to being the reaper's motivation but this would be true even if they went with the dark energy theory. No matter what motivation they came up with it would be new in relation to the reapers since they spent the majority of the series purposely avoiding their motivation. At least the motivation they came up with is a theme that is consistently present in every title of the series. Organic-synthetic conflict has been a part of each Mass Effect, it isn't a theme they just came up with at the last moment.
after all the build up its just lame to learn that the reapers (very menacing creatures like Sovereign and Harbinger who mock organics and think of themselves the highest) turned into slaves of the catalyst who is just an AI basically a mistake by some stupid race
While I may not agree with referring to the Leviathans a 'stupid race' - far from it, imo, I definitely have to agree with sentiment of the starbrat ruining the majesty of the reapers. That's actually a large reason why I hate the starbrat's existence, at least in its presented form. I think it could had been presented better without belittling the reapers... but sadly this is what we have. Like I argued earlier, the mere existence of the starbrat brings with it many contradictions. Still, I have no issue with its logic. Doesn't mean I think they shouldn't scrap it entirely though. Thanks, again, MEHEM.
Coincidentally, the Leviathan's themselves see no mistake in creating the catalyst. It does exactly what they programmed it to do.
its just disappointing and nonsensical especially with Harbingers and Sovereign attitude in the previous games..
Well the starbrat ITSELF, I feel, is contradictory to the reapers... its MOTIVES aren't. In fact if you look at all the taunts Harbinger throws at you in the second game you'll see that its actually surprisingly consistent with their motives.
“We are your genetic destiny.”
“We are the Harbinger of your perfection.”
“We are the Harbinger of your ascendance.”
“Evolution cannot be stopped.”
“Embrace perfection.”
Here's a few lines that aren't delivered in the game but are still present in the game files:
“You fight your own rebirth.”
“Thank us. Beg us for immortality.”
“You insult a future you cannot comprehend.”
“You are the one wasting lives.”
“You challenge your own ascension.”
“One must not destroy the nation.”
An unused but interesting line from EDI on the collector base:
“This explains why the captured humans were rendered into their base components. Destructive analyst. They were dissected down to the atomic level. That data could be stored on an AI's neural network. The knowledge and essence of billions of individuals complied into a single synthetic identity. The ultimate goal would be to upload all humans into this reaper mind. “
Lastly consider what Legion tells us after we destroy the base.
“The reapers are more your future than ours.”
“Your species was offered everything geth aspire to. True unity. Understanding. Transcendence.”
All of this, from the second game, fits in rather nicely with the reaper harvested in the third game. Though one could argue this is a case more for their METHOD rather than MOTIVE - but it still doesn't actually contradict it and it fits well enough regardless. Yet people act like this idea of reapers "preserving" us is something only presented in the final minutes of the game! It's like I said earlier the ending makes more sense when you take into context with everything else. You have view it as a whole instead of just those last few minutes.
It's easy to forget some of these details because of how long time passes since you played through them by time you reach the ending. Which, by the way, in my own opinion, is a sign of a poor ending. They should had made more effort to bring these points back up and not rely on the player to just remember all this **** and piece it together themselves. Rather then spit out a 10 minute summery and explanation at the ending they should had made more effort to bring all these details back to the surface to jog the memory.
And the worst part? that he somehow wants to change things now?!!
Well, he doesn't necessarily WANT to. He doesn't seem too eager about the destroy option nor the control option. The only ending he seems to actually favor is synthesis, which isn't something he just NOW tries but he explicitly says they've tried similar solutions in the past but it didn't end well. The crucible changes it, opened up new possibilities. It's willing to change because there are new options presented to it. To criticize this is to criticize even Shepard. How many times in the trilogy does Shepard start with one goal but can change objectives at the last moment when new data presents itself? Many times.
I know with the extended cut endings its clear that all three endings result in good outcomes (with the right EMS) BUT it still doesn't make sense to me synthesis (Sarens vision) and Control (TIM) go against everything Shepard whether renegade or not stands for
This is all rather subjective. I've heard very excellent cases made from fans of why their Shepard goes for synthesis and control. Shepard's mindset is very much up to the player to decide, afterall. Personally I always go with destroy but I've heard good arguments for all endings, even refusal. I don't think any choice is 'wrong' or against what Shepard stands for since what Shepard stands for is wildly subjective and up to the player. You and I both choose destroy, for example, yet chances are that MY Shepard's reasons for doing so are different from yours.
Side-note but it always amuses me to see people refer to the endings as Saren's ending or TIM's ending. As if that actually takes away from the endings value or credibility. What, because they were antagonists that means any philosophy they had was inherently wrong? You can't judge a view solely off the merit of the person who has it. Control is not made any more or any less positive or negative by the fact that TIM believes in it. Synthesis is not made any more or any less positive or negative by the fact that Saren vaguely comments on it once in the final confrontation.
I should hope those that choose destroy do so for more substantial reasons then just the principle of not choosing something TIM/Saren might had endorsed. 
I always headcanon that he is Harbinger and just trying to indoctrinate me (looks like the kid on earth) and buying time for the reapers and that destroy is the only right choice
One has to wonder then why he would even bother activating the elevator that brings you up to the very device that can destroy them, and then actually telling you how to destroy them, if it was all a ruse to buy time. Things would had worked more in its favor had it just left Shepard passed out on the floor by Anderson, far away from the means of destroying the reapers. 
MEHEM is my headcanon. A bit limiting but since I prefer destroy anyway it works well enough for me. Though I have to admit its a bit ironic that I use it given that one of my biggest complaints about the ending, at least pre-EC, was the fact that there was only one ending to choose from. [Cough]Hypocrite[/cough]
My issue with Control was that it was never presented as a viable option. At best you got to keep the Collector base in ME2 which was a decision that was painted rather negatively with even the pro-Cerberus Miranda, pragmatic Mordin, and otherwise nihilistic squad members all talking about how bad an idea it was (plus the game presenting TIM as a suspicious lunatic). In ME3 both Paragon and Renegade options in the TIM conversations talk about how no one can control for various reasons. The whole TIM arc comes off as a parable of why Control shouldn't be chosen which makes it odd that suddenly it's presented as a viable option -- ranked above Destroy no less, EMS wise.
That I do agree with. I argued that the control ending was always being foreshadowed, not that it necessarily suggested it was viable. One of the big reasons why my Shepard always chooses destroy is because he doubts this fact, actually. That doesn't mean the option for control wasn't being heavily foreshadowed to us throughout the game, regardless of rather or not it would actually work. Also, incase its brought up against me, I never said Shepard believe control was possible either, only that he doesn't necessarily voice opinion AGAINST it. Not the same as admitting it being possible. Just because I don't view renegade Shepard as 'anti-control' doesn't mean I think he actually believes its possible.
It could work if we had the option to work with TIM and we wasn't a loony mook captain, or the conflict against him didn't have the ideological undercurrents. Or maybe if executing Control actually involved the methods TIM discovered on Horizon (no TIM you don't piggy back the Indoctrination signal or whatever, you have to touch these electrical spark thingies that exist aboard the Citadel for some reason).
I would had liked that as well. Infact I would had loved it if the ending choices were presented to you by crucible scientists or perhaps the prothean VI. That alone would had solved so many problems for me. That being said I used to be REALLY heavily against the turn Cerberus takes in ME3... until a few forum goers opened my eyes to The Illusive Man being an indoctrinated tool for the reapers since the very beginning of the series. It made me see it in a whole new light. While I would had still preferred him being like you describe, I do now have more appreciation for the depth of the character. Cerberus isn't "just a baddie to have more mooks to fight" like I originally thought and actually holds some lore significance.
In case anyone is reading this who was part of that conversation, btw, thanks again for explaining that all to me. Made Cerberus a lot more interesting for me. Just ashamed it took me so long to see what was right in front of me... Everything in hindsight, right? lol.