Going to make two points here. 1) How the Catalyst lies but, more importantly, 2) Why I personally think it may have been intentional and kind of a "case in point" coming directly from ME1. Note that while I don't think the endings are perfect and needed improvement in several areas, and was let down by the concept of it, i'm not totally against them either.
-Catalyst says that it "preserves" species rather than destroy them.
Vaporizes little boy. And then has the nerve to take his form.
-Says you won't survive if you choose "destroy" because you are partly synthetic.
Shepard takes one breath at the end, so long as certain requirements are met.
-Catalyst says creations will always rebel against their creators.
Sure. Like the Geth, who rebelled against the Quarians. ...After the Quarians realized they could think for themselves and tried to destroy them, at which point the Geth, for some time, refused to even fire back at their creators. Even after driving them from their homeland in self-defense, they spent time rebuilding it FOR their creators. And like the ever-so-rebellious EDI, who, after gaining the ability to make choices on her own, chooses to protect Joker at all costs. Granted, there were rogue AIs in the previous games, but let's face it. The Geth, a feared spacefaring species, is a much more potent example than that one rogue credit-stealing AI hanging out on the Citadel in ME1.
-Says that Shepard can successfully throw his/her consciousness into a pool with every Reaper in the galaxy and control them.
Shepard couldn't stop him/herself from shooting Anderson when the Illusive Man, with a weaker will than Shepard, partially indoctrinates him/her. Go on. Try to control the Reapers. And when you fail, the reaping will continue...without you there to stop it, I'm sure.
-Plays synthesis out to be the best option.
I won't lie and say that this isn't what I chose, although in hindsight, I regret it. It yanks the genetic diversity away from species in an instant, really. And it might just be me, but I don't see how combining synthetics with organics eliminates the need for synthetics. Unless people's processing powers and through the roof to where they can pretty much do everything that the "all-knowing" programs could do, they'll still us AI.
Thing is, it seems that the Catalyst lies or makes some HORRIBLE error in judgement no matter what ending it tells you to pick. Kind of like it's horrible idea to wipe out organics.
Honestly though, I think the whole point is that the Catalyst was lying or was simply WRONG, or both. There were rogue programs in previous games that were self-aware, but they were still just computers in the end. They were wrong. The Catalyst is really nothing more than a program created to do a specific task, and it flipped it and went off the deep end. It's the epitome of WHY venturing into making self-aware synthetics was against galactic law.
Because you eventually get children who think it's cool to wipe out the entire galaxy every 50K years.
Sorry if this has all been said before. Probably has, but thought I'd share my thoughts anyway. Ending is WAY too open for speculation as it is and is very discombobulated, so I'm waiting for EC to see if that's the point they were trying to make.