How is the existence of the AI hard to understand? The AI existed in the Citadel the entire time and was the guiding force behind the Reapers through all three games. That it only revealed its true nature at the end makes perfect sense from a storytelling point of view. I understood this even before Leviathan came out. One of my problems with the writing at the end was how damned heavy handed it got spelling all this out.
There were no new characters introduced at the end of ME3. We were merely being shown what the Citadel actually is--a respository for the Catalyst.
If the Catalyst was on the Citadel all the time (and has been since time immemorial). How is it that Sovereign needed to attack the the Citadel in order to bring the reapers out of Dark space in Mass Effect 1? Couldn't the Catalyst just of pulled them out itself? Or are we to presume that an AI that's capable of changing the very fabric of the universe was somehow incapable of doing this?
It's all very well to introduce new concepts to an ongoing story, but the have to be consistent with what's come before.
I thought the game explained that in the end: for the same reason it couldn't make the final choice that it left with Shepard. That is, the AI only ever worked through its Reaper intermediaries like Harbinger and Sovereign. It could only direct, not take action itself--presumably because the AI didn't have direct control over the Citadel's systems.
And, of course, Sovereign only needed to attack the Citadel because there were people defending it. On that score, the game seems consistent with itself throughout. It would have only been inconsistent if, in the final moments, the AI didn't need to use an intermediary like Shepard to actually pull the trigger.
It's also worth noting that the AI and the Citadel were not capable of changing the fabric of the universe. That ability was given to it by the Crucible, which the game points out had never actually been completed before. Everything in the game points to the AI on the Citadel being limited in scope to coordinating the cycle, not actually doing anything itself. Now, we could argue as to why, but the game answers these other questions.