The Catalyst is in the Citadel it is not THE Cidtadel

To avoid any kind of plot hole on the subject, it is sufficient to say that, "during the events of me1, the catalyst does not control the citadel". The end.

Why? There are hundreds of possibile explanations.
The catalyst is dormant.
The catalyst is unable to control the citadel and/or to perform other material actions.
As you said, "the citadel is part of me" can simply mean that the citadel is the physical structure on which it is installed. Nothing transcendental.
The prothean somehow "hacked" the catalyst. Vigil said that the prothen scientits "altered the citadel signals". Vigil exact quote. So, if Citadel is (part of) the Catalyst, it means that the Prothean scientist altered (part of) the Calatyst's Signals.
Etc etc.


It is quite annoying that people try to create plot holes (meaning "contradictions" "illogical things that do not make sense") even where there are only omissions.

Something not explicitly explained is not something bad/illogical. This is the crucial point of the whole "ME3 ending makes no sense" misunderstanding, imo.

1. premise: the catalyst being unable to perform material actions is just one of the possible expanations. The are others (es. catalyst is dormant, hacked etc)

2. we are talking about the events of ME1. At the end of ME3 the reapers take back the citadel, and the catalyst could have been restored in some of its material functions

3. The catalyst most likely raised the platform. The platforms activation can be part of the crucible functionalities, of the catalyst doing, who knows. But let's say that the catalyst can perform basic actions like raising and/or activating little platforms. We see it. But iInducing that, because it can activate platforms, so it should be able to activate the mass relay to the dark space or open/close the arms of the citadel is .. bad induction, imo. It' like saying that because I can lift a pen in my bedroom, I can make my home fly. Not necessarly true.
Or maybe he could control the citadel during ME3 ending, but Shepard temporarily "overruled" its control over the citadel primary functions when he activates the panel in order to open the arms and dock the crucible. Who knows.
There are hundreds of possible explanations.

Is your phone a super intelligent AI capable of nearly wiping out an entire race from before the Reapers existed?  No?  I have my doubts about your conclusion.

The catalyst super-abilities are are related to anthropological and historical analysis, strategy and calculation, evaluation of variables, and long rage mental influence/control.

This is the purpose for which it was created, and this is what it does.
He wasn't created to DO things, perform ACTIONS in the material world (like EDI was), but to study an historical pattern and find a solution.


As for his material abilities, controlling things and so on, we know very little.
1. 
initially, he used pawns to do its studies and destroy the leviathans
2. he used the reapers to wipe out civilizations and the collectors to create new reapers
3. he used the keepers to manage the citadel
4. he needed saren to get control of the citadel
5. he needed shepard to activate the crucible


In the light of this, we can safely assume that it has some kind of physical limitations. It surely doesnt' have the ability to always control/make all the thing:  on the contrary, he need others to do the "handiwork".

We saw that the catalyst can raise a platform. Ok. Is this enought to say "if it can raise a platform, than it must necessarily be able to do infinitely more complex actions (like directly open/close the citadel, activate a mass relay ecc.)? And if it doesn't, than we are facing a huge, illogical, plot hole? IMO, no.

1. maybe it has no other choice. Maybe he is something super-smart but at the same time super-weak. Maybe it is the synthetic counterpart of this buddy, and need others to take care of itself


 2. Vigil said that the reapers "go dormant" between cycles, in order to preserve energies etc. Maybe the Catalyst (which is collective intelligence of the reapers..) used to do the same. Why not. Maybe the sovereing signal was the "wake up" signal for him too, but this time the signal was uneffective, because of the prothean scientists

3. Maybe he was perfectly aware about everything going on in the Citadel, but:
a) he is unable to perform complex, material action... so he still need pawns to act
b ) he was able to control the Citadel, until the prothean scientists "altered the Citadel signals" and so remove the keepers from the reapers control.

Indeed, though I use John P's Alternate MEHEM.  It removes the extra video and voice acting that weren't present in the game.  It does keep the memorial scene.  You can choose to have the choices (which I assume means Shepard survives them all) or just press a button and Destroy happens.

But there are no lore breaks. The game swings into the ending just fine.

The catalyst believes that synthesis will end the organic-synth conflict.. maybe he's wrong, or maybe not. Maybe all his psico-historical analysis of the problem is flawed... who knows. It's the Saren path. Organic and machine intertwined.

I don't like the reapers running around too, but this was TIM goal from the beginning. It's a rational option, an high risk-high reward option.

"why would the catalyst create a "solution" that destroys it and the Reapers?" The catalyst create nothing, the crucible creates this solution: it was build fot this very purpose.
The moment the crucible docked on the citadel, the reapers are done, finished, defeated, "they won't work anymore", and even if the crucible is not activated, they will be no threat for the next cycles.

If Shepard turn down synthesis or control, the catalyst has 2 option:
1) be eliminated by this cycle and let this "special" cycle find a new solution for the chaos problem
2) be eliminated by the next cycle and let others find a new solution for the chaos problem
And he obviously prefers the first option (although it warns you that it is not a good option)

That's a definite reason to assume Synthesis might not be the rainbows and unicorns ending the Catalyst portrays it to be. If you're a first time player of the MET, you might conclude from Saren that Synthesis is something to fear.

Again, if TIM thinks it's a good idea, it's probably best to run the other way. "Big Brother" is not anything I'd want to see played out.


Right, I sometimes lose sight of that versus my pet theory that the Catalyst created the original idea of the Crucible and left the plans around for some previous cycle to find.


Shepard wouldn't know that and a first time player wouldn't either. Without that foreknowledge it would seem as though Shepard were dooming the galaxy to endless cycles. It's a big assumption that Liara's plan to seed the galaxy with the Crucible plans would work.

But I don't like destroy. Why would I want to commit a criminal act of mass genocide against untold billions of innocent sentient beings who I helped save earlier in the game? Destroy is an utterly nihilistic, pure renegade option.

I'll keep using MEHEM thank you, and if MEHEM were outlawed I'd have to reluctantly go back to choosing the control ending.

To be fair, all 3 ending choices are renegade choices.