My pet theory is still that the keepers were behind it. Who else knows the citadel better? Who else has the enormous technical expertise to conceive of it? And who else has more of a reason than anyone to want the endless cycles to stop?
Keepers were well established as being pretty much husks that had gone to trade school. It would have been more interesting to have the Catalyst depicted as one, though. Then again, taking the form of the child that's been haunting Shepard reinforces the idea that the Catalyst was (while not in control of Shepard) making a really hard sell. "I know you really had your mind set on destroying us, but how about you look at this shiny new model 2186 Synthesis. It's way better, oh and no one dies. Ever. Everyone becomes a glowing Highlander, except no swords now that Kai Lang is dead. I promise. I'm a child, would I lie to you?"
The more I look back, the less bad I find the ending. Not great, like the first two games, but it's clever at least.