The premise is not that synthetics simply rebel or oppose their creators; it is that they wipe them out. Neither of these happen. Not only do the Geth decide against wiping out the Quarians, though they did kill many, but they planned to upload into and chill out in their superstructure. (Ooh, what if that was actually part of the game, not just mentioned, and it was basically a Geth Reaper?!)
But doesn't this premise start with rebelling? This is what happens first, so the wiping out could potentially occur afterwards. I'm a bit torn here because of course you are right, the geth did not wipe out the quarians and that makes the Catalyst look wrong about it, but on the other hand the Catalyst works with this logic that all synthetics must eventually surpass organics, because that's just how they develop in order to be efficient enough for organic desire. I can understand that from its point of view, but then also people who say it is stupid to think like that. I guess the problem is as folks say, that while it's likely right that synthetics always surpass organics at some point, it doesn't take into account that not all synthetics might want to wipe out organics (however that can maybe be a faulty programming of the Leviathans, dunno). Which of course is the problem many here have with the Catalyst's logic, but I do see where it's coming from (more on that later).
And just in the case of rebelling first, I think the Catalyst was right in the geth's case. Afterwards they also just react like any organic would, trying to survive. And I don't blame them at all.
A Geth Reaper sounds interesting and yeah, it would've been nice to see it.
This is tough to answer because I, the player, was sure the Catalyst wasn't lying, but stepping into Shepard's head, I might be concerned that the Crucible was a trap. Perhaps we actually could win conventionally and this was some Reaper contingency plan. After all, Sovereign told Shepard that the Reapers left behind technology for them to find. And, much like the Relays. these Crucible plans somehow survive every cycle. The other thing is that even if I beleived the Catalyst about the Crucible itself, I have no reason to believe it that Synthesis is great. It obviously wants it, which, barring any other information, is enough for me to oppose it.
Unless it's reverse psychology! Oh noes!
Ah, so you also believed the Catalyst as the player? That's what I meant the whole time. The thing with Shepard is just... sure, it could be that the Crucible is a trap, but I'm not sure about the conventional winning. Shepard has seen how much it takes to take down only one of these things, so I and my Shepards never believed conventional victory is possible and it's also not what the game sells us, quite the opposite.
And then we also encounter Vendetta who explains a lot in this regard. Doesn't necessarily mean it's true what it says, but then, we still have no other choice but to let Shepard use the Crucible before this cycle is wiped out too.
I must admit, I've never thought about the plans like that, I like the idea that it could be some weird Reaper plan or trap, on the other hand if this was indeed a trick, then what is its purpose? The Reapers would win anyway, why would they need the Crucible to gain even more advantage? Ok, this is all assuming that conventional victory isn't possible, so... eh, I don't know. There should've been some signs in the game that it is possible to defeat them conventionally. Which would be tough after what we've seen with Sovereign I guess.
And sure, you don't have to think Synthesis is great, I always say each player will make up their mind about this whole thing and which option might be the best anyway, so of course this is totally valid.
As far as the Quarians, I wish there had been the option to point out that it really doesn't matter because all the Quarians that were alive 300 years ago are long dead. I don't know if Geth wear out and die or are replaced like in the Matrix, but it's implied that the programs in Legion were around then. But the current Quarians had nothing to do with that. What they need to do is see this as a restart point.
Anyway, you're right that the current events do no mean the Catalyst was wrong about the past, but the do show a problem with the "always" premise. If the premise is not relevant here, than neither is the solution. Basically, the Reapers aren't needed and can go away. Maybe they will be in the future. In that case, they know where to find everybody.
I think this is a tough one again, because just as back then, not all quarians wanted war with the geth. Sure the quarians that started everything are dead, but what about the ones like Gerrel that still support these views and the war? History repeats itself here.
Yeah, I can get that. I assume I just tie it too much to this logic of the Catalyst I've mentioned earlier. Guess it's machine thinking what it does, I don't know. But if we look at the way it does think, for the Catalyst it's the logical conclusion that synthetics surpassing organics would always result in synthetics wiping out organics.
I'm not saying it's right to think like that, but I get why it would.
It could be tied to maths, like coming from the Logics field, Inference, and then something like Deductive/Inductive reasoning. Maths is not exactly my favourite topic (I was really bad at it in school 
), but there are some things that might back up the Catalyst's thinking process and which also drifts a bit into the philosophical field.
Maybe it's also tied to inductive logic programming, who knows (got this from Wikipedia and it sounds quite close to me, but again, I'm far from understanding that crap 
Given an encoding of the known background knowledge and a set of examples represented as a logical database of facts, an ILP system will derive a hypothesised logic program and Machine learning explores the study and construction of algorithms that can learn from and make predictions on data.).
I don't know if it was an influence, but they tried to do something similar to Descent: Freespace, where the Shivans invaded and were wiping out the two major races. In the epilogue, the newly voiced Protagonist explains that they now realize the Shivans do this to keep powerful races from destroying weaker ones. That's not exactly what the Reapers are doing and Descent did a better job of making you potentially sympathetic to the enemy and wonder if the powerful races will choose a different path. On that note, I finally got the second game and got it working and the alliance they form to fight the Shivans is still holding at the start.
I was perfectly fine with sacrificing Shepard. I was not fine with forcing alteration and homogenization on the galaxy in a series about diversity and choice. I don't blame you for liking it. It is clearly written and designed to be the "golden ending."
I do not know it, but it sounds indeed very similar.
Haha, don't get me wrong, I'm not exactly fond of Synthesis. I only liked the concept a lot. The peace, the "understanding each other" part. Well yeah, it pretty much spells "happy end" and I picked it the first time because I liked the sound of it and I also wasn't willing to lose the geth and EDI over it tbh. But the result was a bit too weird for me. So since then it was always Destroy (but mainly of course because it fit my Shepards). But there are good points for Synthesis as well as against it, like with every other ending too. Everyone has to see for themselves what they think is best for their Shepard(s).
1) Oh, please, PLEASE don't start with that "What, you need everything explained?" garbage. You're too smart for that. A plot hole is something which causes logical conflict with what was already established before. Plot holes can be different "sizes" and have different effects on the story. Sometimes a question has a clear answer based on context or common sense. Those probably shouldn't be called plot holes. Sometimes it's not a big deal and we can speculate on what happened. However, this one makes us question the entire first game. Sure, there are theories, but that's too big an issue to be left to wild speculation. It is not our job to fill plot holes for the writer.
2) I mean that the Quarians would win without the Reaper signal, just like I said. They backed the Geth up to Rannoch and that is when the Reapers interfere, turning the tide. Then, once all Reaper influence is removed. the Quarians wipe out the Geth.
As for why the Quarians win here when they couldn't defeat the Geth before, I couldn't really tell you. Maybe it's all those dreadnaught guns they had on the live ships, maybe it was the destruction of the so many Geth in the superstructure. I don't know. It's a great question and possibly even, as discussed in #1, a plot hole. It's not nearly as bad as the one discussed above, but it could be called one.
As for the Catalyst, the past is irrelevant. What matters is the current cycle is different and the Reapers are neither needed nor wanted. Maybe the Geth or some other Synthetic will rise up and be the problem the Catalyst describes. But the galaxy will deal with that on it's own terms. As Legion says, they'll build their own future.
3) I wish they had gone more into what the value of being "preserved" as a Reaper is.
1) Well apparently I am simple, because what I think of in this regard is simple. If the Catalyst didn't do anything in ME1, that means to me that either it couldn't or it didn't want to. I've recently dismissed the didn't want to after some discussion with other folks, but the "couldn't do something" is just a consequence that makes sense somehow. So yeah, maybe I am oversimplifying. But who knows what the Protheans did with their little intervening. Far-fetched? Maybe. Possible? Don't know. But it can just be that. I think. So I don't know if I would call this a plot hole, since it is still somewhat in line with what is happening. At least to me.
2) Yeah, seems I didn't see the situation for the geth as that bad when the quarians hit, but of course it makes sense that it is.
I rewatched some scenes yesterday and I think that is explained in the game by Tali. That because of her fathers' research, Xen was able to develop some effective measurement against the geth, that it overwhelmed the geth with garbage data, leaving the geth more vulnerable and that this was too big an opportunity to pass up.
Guess that sounds plausible then 
3) Yeah, it could've been even more in the game, but Legion talks about it in ME2 as well, that the geth desire what the Reapers want and offer, true unity and so on. I touch some more on that in the next section.
Of course, we already knew that since you started with "you just didn't get it" defense and then rambled on about the Reapers not being bad guys. Oh, I guess I was confused when I thought they were killing everyone.
See, and here's the difference between organic thinking and synthetic thinking I was talking about To you it's killing everyone, which it of course is also to me because it's simply true. But to the Reapers, it is seen as helping/uniting/preserving, all positive terms, they do cannot see the negatives associated with this killing. Likely machine logic again.
And they do all this with a cold efficiency and ruthlessness, but they want to "embrace" and "help" anyone who would like to become one with them. And even the ones that oppose them, because they don't understand how organics cannot want to become immortal. See the dialogue with Legion in ME2 as you've also mentioned it. He tells us that to him it's interesting that Shepard does not want what the geth want, which is the same as what the Reapers offer: true unity, understanding, transcendance (hence their desire for their megastructure). To us, we just want to die whenever we do, we do not want to become immortal or anything along the lines the Reapers offer, we do not want to be preserved or uploaded anywhere, and that's what the Reapers don't understand, just as we don't understand why they think we would want this. Or even why they think they help us ascend. (I mean, I can get that part, but it's not like I'd want that either )
It felt like the main theme was more about how you bring a galaxy together, with the dlcs showing you the errors of past races than about the organic/synthetic dilemma (which is pretty interesting in itself, but I did not see it coming)
I guess we could argue that some things can't be seen coming... I mean, sometimes things are revealed that we didn't see earlier, even in real life, how is that so different in a game? Let's assume something happens and you don't know why. When you find out the reason it's nothing like you imagined. But is that a bad thing just because you anticipated something else? We simply cannot know some things that happened in the past until we are made aware of them.
Personally for me the theme is there, especially since we (the organics) go against the Reapers (synthetics). This is the central point of the games (or at least lurking in the background in ME1/2), and yeah, uniting the galaxy theme is fine and all, but for what are we doing that? To prepare for war and fight the synthetics, ultimately resolving this "everlasting conflict" with the Crucible.
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