1. It's a deus ex machina (in this case, literally) pulled out at the last moment. A major entity- essentially the true villain of the series- is introduced in the last 5 minutes. There's absolutely zero reason for a player to expect the catalyst to be a god-ai-child in the citadel. The existence of such makes no sense within the setting as defined over three games, several books and the available lore. This also devalues everything Shepard- and thus, the player- had been doing throughout the series. It's poor story telling, and is just plain inconsistent with the world they had created.
2. It takes the reapers- something that had been billed as having a purpose that mere organics could never comprehend- and boils their purpose down into one sentence: "Prevent organic races from advancing so far that they create a machine intelligence that would destroy all organic life in existence". They're no longer lovecraftian horrors from beyond, they're just park rangers keeping the population in check. It's not incomprehensible, it's not complicated, it takes less time to explain than Sovereign spent telling us it could not be explained to us. It takes an interesting- if somewhat unoriginal- antagonist and makes them boring.
3. It's lazy: the ending is determined by your choice at the last moment, not your actions before hand. The ending of a game should be the culmination of your prior choices; it should be determined by the decisions you had already made. Just look at BG2 ToB- you got a choice at the very end, yes, but the gritty details of that choice were determined by how you answered questions from Solar earlier, from what you did earlier in the game. The "push a button, win an ending!" mechanic is just outright lazy. The endings in ME3 are all exactly the same once you press that button, regardless of what lead up to it. The endings weren't shifted (even slightly) whether you were paragon or renegade. Imagine if, upon controlling the reapers, that ending branched out in three directions (paragon, renegade, neither) based on Shepard's tilt? There's nothing like that in the ending though, it's unchanging.
4. There's no option to interject and make your own choice. In the end, you're only accepting the choices offered to you. This is always true within a game, but part of the art of making a good choice-centric game is making those choices feel like you made them yourselves. The game completely fails to accomplish that with this ending; you get to the end, you're told "Pick red, blue, or green" and that's it. Shepard has no option to reject those choices and make his/her own. It's all completely arbitrary, and there's no reason given to believe that you're actually constrained to those choices except because that's all the game has options for. You can't even try to reason with the entity, Shepard just nods and accepts fate. That is so amazingly out of character that it completely destroys Shepard as a person, as a hero, as an agent of the player. My Shepard had not once accepted destiny- fuck, the whole plot of the series is about rejecting our pre-determined destruction! Shepard does everything they can to ensure sentients have their own choices to make, their own path to follow, not matter how many obstacles- even by allies- were placed in their path. My Shepard had always tried to reason with everyone, no matter how much it might appear to be a fruitless endeavor; s/he can even talk two indoctrinated people into taking their own lives to fight the reapers, even though indoctrination is supposed to be irreversible and pointless to oppose.
5. This is the big one (save the best for last and all that): the Mass Effect series had been about choice. When you imported a Shepard from a prior installment, you weren't importing the character (you could remake your skills or even your class with every import, your equipment never carried over, and only a limited amount of your prior resources made any showing at all), you were importing the culmination of their choices to date. Your choices were supposed to matter- what you did about the rachni queen, the geth, the genophage, if you saved the council. How you solved the personal dilemmas of your friends and crew. If you preferred to leave a wake of rubble behind you, or tried to reach a compromise to make everyone happy. Whether you stuck by your friends, or betrayed them for the greater good.
Many of the decisions you made were not about the immediate future, they were about determining the long-term future of the galaxy. The ultimate results of that outcome was presumed to become apparent in the time after you finished the game. Curing the genophage would have no galactic consequences in the few months that ME3 covers; people deciding whether or not to cure it did so on the centuries later outlook for what they thought would be best. The geth and quarians getting along or not would have no significant change in the short term, but in the long term, they could become a juggernaut within the new galactic civilization, or recant back to being a pariah. The rachni could doom everybody, or become another benevolent participatory in civilization. And so on and so on.
The problem is, the ending completely invalidates all of those choices. None of them mattered anymore once you got to that ending, because they all ignore and then promptly erase everything you had done beforehand. I had invested myself in making decisions to affect the future of the galaxy, not to get a higher war score. The ending stripped that from me and everybody else.