Holes such as: Low-EMS ending states, inclusion of Refusal (especially via shooting the Catalyst), and oh yes, the fact that IT requires hand-waving entire parts of the ending that prove it wrong (Control and Sync being positive overall endings) for it to fit in.
What I see here is blind acceptance of what people like/want to believe, and scrutiny only for the things they don't.
A dismissive or skeptical attitude towards the Control and Synthesis choices and the slides that were added in the Extended Cut hardly constitutes a "hole in the argument".
We use our experiences during the Mass Effect trilogy, the lessons we have learned over the course of the games and our knowledge of the universe and lore to make our decision. Less than three minutes before meeting the Catalyst, Shepard was referring to the idea of "Control" as a potentially disasterous pipe dream. Shepard was arguing that we should not risk the future of the human race - let alone the Galaxy - on such a pipe dream, given what we know about the Reapers and their methods.
A couple of minutes of perfunctory exposition, circular logic and vague assurances later, and suddenly it becomes a good idea? I think not.
The same rationale can be applied to Synthesis; we have seen a union of flesh and steel in the Mass Effect universe many times before. It never ended well.
So the ending slides added in the Extended Cut seem (emphasis on seem) to show that it all works out in the end. So what? Does Shepard know this at the time he/she is required to actually MAKE the decision? No. Which means that the "evidence" of "positive outcomes" in the Extended Cut ending slides are entirely irrelevant when it comes to actually making that decision.
Plus of course, it's not unheard of for indoctrinated people within the Mass Effect universe to actually BELIEVE they are doing the right thing; in fact, it's something of a recurring theme. The Illusive Man believed wholeheartedly he was working for the good of humanity and against the Reapers, yet he was their thrall. Saren believed with 100% certainity that he was trying to save "more lives than have ever existed". Yet he was indoctrinated, and implanted, and ultimately dead wrong. They both had a positive vision for the future, yet if their actions had succeeded, so to would the Reapers.
The Extended Cut slides (added as late to the game as they were) show what they show. Take them at face value, believe what they show implicitly and without question if you want to - that's up to you. But don't believe for one second that they show absolutely everything, or that they rule anything out. You have CHOICE, remember? More than you know.