Sorry for being imprecise. There are a lot of aspects about the ending that I think are very problematic, some of which I mentioned here, lots of which I did not bring up because the OP didn't. For example the question of why Shepard has to die the way he/she does, e.g. in the control ending, which is currently discussed (again and again...one might say
) in the "The stupidest reason to hate the ending." thread.
I was referring to the question of "why does the catalyst allow the control ending?" which I think can be explained as you did (with some stretches, as mentioned in previous posts, but that's okay).
As to the question why Shepard dies the way he/she does... because Bioware chose it 
But seriously, I think these endings need to be looked at with a certain emphasis on transcendence. In both Control and Synthesis, Shepard becomes a whole different thing. There may not be any explainable, or even logical reason for why it happens the way it does, but the crucial points still stand: Shepard has to give up the physical form, in order to either become the new consciousness of the Reapers or to sacrifice his whole essence of who he/she is.
I'm not saying I like these two options btw, but these two happen on a "higher" level than Destroy imo and need to be taken in that way I think. Maybe this could also be why it feels so out of place for many, I don't know. A lot of the ending just has to do with this whole "Energy" thing. The Crucible is able to deploy a huge amount of energy, Shepard's energy is what's needed for Synthesis. It's not really something you can grasp, if you know what I mean.
Why it allows Control, yes, same as with Destroy I guess. Something prevents it from acting against the Crucible, it keeps saying that Shepard (or all organics) has altered the variables, that the Crucible changed it and made new possibilities available. It says "It is now in your power to control us" (Low EMS).
I think it's funny because when you preserved the Collector Base in ME2 Control makes so much sense imo. You'll get the Human Reaper mind from Cronos when you preserved the base, and this is what makes Control actually possible in Low EMS.
For High EMS I'm just gonna assume that one of your assets was also capable of controlling Reapers. AFAIR the Protheans were convinced the Crucible could be used to both destroy and control the Reapers as well.
In conclusion, I think we might never know why exactly the Catalyst can't act on the Crucible changes, but it is what we got.
(Btw I just remembered, there's also a really interesting thread with theories about exactly those things, the Catalyst, the Crucible and the Citadel, and how they work together, it's here.)
I think that a "lack of closure" actually has been brought up as a point of criticism, but on this I agree with you that this is rather subjective. Do we need to see Tali in her house on Rannoch, with the stone Shepard gave her in a display cabinet? It would have been a better slide than her (or another Quarian) simply standing around, but, well...
I also agree that a "lack of exposition" is not a valid criticism for an ending that is coherent, quoting myself: "Since most of ME is told from Shepard's perspective, it is narratively coherent not to answer all the questions that the audience may have, like what the true goal of the reapers is or what the catalyst is or how the crucible works, if Shepard never gets a chance to find out."
I've seen the "lack of closure" comment many times. I do get that people want to see their favourite characters once more, all together, united with Shepard etc etc, but they have to see that Bioware specifically chose to NOT spell out the outcome. That's why many times they sound just butthurt because THEY didn't get what they wanted. Reality is, not everyone can be pleased. Bioware does a lot to please fans and listens to a lot of feedback, but in the end there's always too many opinions on what should've or what shouldn't have been in a game. What's important is that they stick to their own vision.
Anyway, I completely agree with your second point. I really liked that I truly became Shepard in the end, there was no time to ask the Catalyst a million questions, it was only time to act and end the war! 
My problem is that the ending does try to give an exposition that results in a factor of 20 to 50 more open questions than it tried to answer. There are several ways to cope with that as a player:
- Ignore everything the catalyst says as a lie and choose the destroy ending (or install a mod that does that for you, automatically).
- Accept lots and lots of new open questions thrown at you right at the ending, because it's all a big mystery anyway (the biggest being: how can blue aliens with squid hair be so attractive? I mean, really?
)
- Make up answers on your own, lots of answers, with ingenuity. Maybe proves that you should try to write your own sci-fi novel? (That would seem to apply both to you and the OP
)
- Complain. (That's me.).
Why? In short: If somebody (like an author) tells me they are going to buy sweets for me at the supermarket (do an exposition that answers some of the biggest questions of their plot), and then come back empty handed (or with green vegetables), I'm like "you did not have to promise that, you did not have to try it at all, but if you do and fail, I can point out that that's a failure, alright? By your own standards".
ME3's ending is unpopular. Being unpopular does not prove that an ending is badly written. In case of ME3, all the open questions/plot holes/inconsistencies/contrivances that have been brought up, they do. I don't think this is merely a matter of taste, but choosing how to cope with it certainly is, meaning that it doesn't have to trouble everyone playing the game, of course.
1. Well I choose Destroy anyway, any day. But I do believe the Catalyst is answering to its best knowledge when presenting the choices.
2. Hahaha, I don't really have that problem with the blue babes 
3. Oh no no, I could never write something like that, but I do enjoy thinking about answers, and speculate with others
4. Believe me, I also complain, everyone complains, it's natural. Maybe not so much about ME (it's still only a game, hehe), but other things.
I guess we can agree on everything else you said here, I'm just thinking that maybe with trying to answer more of the questions that rise up, maybe some of them can be answered in a satisfying way and that it makes sense.