Yeah, a deus ex probably wouldn't have irked me as much if it actually fit. I mean, it still would have been annoying, but this one didn't even slot into the universe very well.
(I think indoctrination theory is a silly way for fans to read far more into the story than Bioware ever intended, or imagine an ending that never actually happened. Bioware doesn't normally operate on that type of level. And I don't see any irreconcilable or disbelief-unsuspending inconsistencies in the ending up to the point where the Catalyst comes in. Bioware has said that the ending DLC will extend, not replace the ending.)