It's done. That said, no it doesn't bother me. I accept that he is a flawed A.I. stuck in a logic loop. Admiral Hackett himself reiterates that conventional warfare isn't possible. Whether or not you choose to believe the A.I. child is up to you.
At the end of the day, EMS is a gameplay mechanic. No matter how high you make it, once you reach a threshold, your fleet really doesn't become any stronger in the canon. If it did, then that would be a different story.
Come the end of the game, Shepard has nothing else to go on but hope and a choice. The fleet's purpose is the Crucible. The entire game is about building and escorting the device; and depending on your EMS, how much damage it takes as it makes its way to dock with the Citadel. I'm very comfortable with the fact that the A.I. child reveals himself to be stuck in a logic loop he can't recognize for what it is. Or maybe he does? Either way, the choices in front of you exist whether or not you choose to believe the information given to you is accurate. Which is nice now that Shepard can choose to act on the limited information or stand and die - because again, it was stated before and during the ending that conventional warfare is not a solution. If it was why even bother with the Crucible?
I can accept that. To make conventional warfare and option would make me raise an eyebrow about the Crucible as a plot device at all. To that end you have to question the Crucible and whether or not you liked it in the game at all. Odds are if you're still unhappy after the EC, you'll say no.
Is the ending perfect? No. I still don't know how Anderson ended up at the end before me, or where the Illusive Man came from. Do I think the Normandy evac was awkward? Yes, somewhat, but I can reason with what was going on around it and accept the possibility. Beyond that, the A.I. child's voice is the voice of the actual A.I. rather than the interpretation it was trying to make for Shepard for his initial conversation. That is neither a big deal, nor surprise to me.
At the end of the day, what the Catalyst said was true. The endings speak for themselves, and the Mass Effect team made them as direct as possible. What subtle hints there are to anything otherwise is, to me, the reflection of a desperate mind looking for reason to argue against something it still doesn't find satisfactory. If that's the case, better luck elsewhere. I look forward to giving Bioware my attention again - albeit cautious.