Ben Kuchera weighs in. Reading now.
Okay, so he deals with three perceived primary arguments: 1) Deus Ex Machina, 2) Inconsequential Choices, and 3) No Good Ending. I think we can ignore 3) since it's kind of a stupid thing to complain about the ending in any case, but I don't think he deals adequately with 1) and 2). He also throws in a bit about "Isn't it great we're having this conversation about a videogame", which I find a bit pithy, but whatever.
Deus Ex Machina: Pointing out that the Prothean superweapon was set up incredibly early in the game, as was the kid; additionally, that Prothean/Reaper technology functions indistinguishably from magic in the first place.
I agree that the Prothean superweapon was set up early, but that doesn't mean that the Catalyst (as an entity, or more accurately, as a Space Wizard) was set up early in the game. I think everybody realised where the kid came from, but just thinks that it was incredibly ham-fisted and clunky. Additionally, Ben seems to think the Relays and the Citadel are barely understood in-universe, and that the Biotics are hand-waved away; I think they fall more on the 'explained via SCIENCE' side of the spectrum, admittedly via the codex and Eezo, which is itself a maguffin, but at least a believable one. There are differences in levels of suspension of disbelief, I think, and the giant magical space-rainbow-magic just crushes suspension far too hard.
Inconsequential Choices: Choices do matter, but they matter prior to the ending, and merely because the ending doesn't factor them in or display them explicitly doesn't take away from their personal meaning to you.
This is a fairly confused point in my opinion and I think it fails to take into account the extent to which closure is a meaningful and required part of any given story, or journey, or adventure. I agree that choices do have a major impact in the game, especially over the course of the two prior games before ME3, and they do powerfully affect the different journies that different Shepards can have. The main problem, however, is that it ultimately lacks a true sense of closure; most of what your past decisions do is crunched up into a small set of numbers and fed into the glorified progress bar that is Effective Military Strength. Ben ridicules the idea of disliking the ending because the game 'doesn't give you a rehash of what you've done', but I think this is a very valid thing to desire; an acknowledgement of consequences for your actions. As it is, the game completely glosses over almost everything that you've done. Ben further notes that 'what the game doesn't do is rub your face in your choices' (specifically regarding the Colour Choices at the end of the game), but I don't think it even really says anything meaningful
at all about your choices given how similar the ending cutscenes are and how non-informative they appear.