This is probably the most well-written and insightful pro-ending posting I've read.
That being said, I still don't like the ending. Not because I'm stubborn, but because I disagree with enough of this article that I remain unconvinced. I'd like to argue a lot of these points (in a civil manner of course, I think I'd thoroughly enjoy having lunch with the original author and discussing and debating many sciency and philosophical things), but I'll keep it trimmed down to general complaints to keep this from becoming too much of a wall of text.
First, as has been posted before, a lot of the first segments come across as logic smoke-and-mirrors. I very much understand the ideas (or the math) and am familiar with concepts such as the Kardashev Scale, the Drake equation, end-of-the-universe scenarios (Big Crush, Big Rip, universe-scale entropy, etc etc), the technological singularity, quantum entanglement, and so on. Unfortunately, much of this is never referenced within the ME series.
MEs writers are big nerds like us, they took the time to give a plausible physics explanation for all the major concepts and technologies used in the game, whether that be through dialogue or a codex entry or what have you. They explain how mass effect fields work (eezo makes mass-altering fields), how the relays work (effectively create massless corridors), how you need fuel to fly between galaxies even though there's no air resistance in the void of space (engines fire forward for first half of trip, backwards for second to decelerate, peak speed is only achieved momentarily at halfway-point), how older comms worked (data sent through relays), how the new comms work (quantum entaglement), the list goes on.
However, they NEVER included content on the Kardashev Scale OR the Drake Equation in any of the dialogue or codex entries that I was exposed to. If its in the game somewhere, please, refer me, I'd honestly be interested in reading/listening to it. They do indirectly touch on the technological singularity once or twice (both Legion and Javik do if I recall), but they never refer to either of the two main concepts you used to explain the ending. I didn't consider the Kardshev scale in my appraisal of the ending not because I wasn't familiar with it, but rather because THE GAME never claimed familiarity with it. Perhaps BioWare simply assumed familiarity with these concepts. Their track record (of at least attempting a scientific explanation behind just about everything) stands against that. Going against evidence and assuming they did assume familiarity, it supports that the ending WAS poorly done, because it incorporated new concepts that were never explored within the game itself.
I'll use a little device called Occam's razor here (since the device has become wildly popular on these forums as of late for some reason). Stack up your article against IT, and, surprisingly, Occam's razor favors IT. Why? Because both the article posted and IT make some pretty large leaps and assumptions about the ending sequence. The "proof" used to justify IT, however, is actually present in the game. Your evidence is not. Ergo, less assumption and logical leaps are used to support and defend IT because the evidence has already been established within the universe. I'm not saying this makes IT true (that's not even the purpose of Occam's razor, a point many here on BSN seem to skip over), just saying that from a logical leap perspective, this article is unfortunately doing no better.
Also, the focus of your article seems pretty disjointed. The first few sections go into a bunch of scientific soft-shoeing (albeit well done soft-shoeing) to explain the "deeper meaning that everyone missed" in the endings, and then the rest turns into a Mythbuster's style "Fact or Faked," with the writer having (likely inadvertently) cherrypicked some of the worst misconceptions and arguments to dispell and provide support to the meta-thesis (which would be "the ending was good", I guess?), often through proof by contradiction, or by missing the point entirely and getting lost in debating a nuance of the issue.
Also, your final thoughts were surprisingly caustic, in my opinion. I've purchased all three games and all DLCs as well as plenty of other ME memorabilia, and although I hated the ending I never for one second entertained the idea of returning any of my purchased goods. I also never filed any complaints with the BBB or the FTC. Although I never donated to the Child's Play charity (I'm a poor college student, I don't have two pennies to rub together) I did express approval and support for the idea of performing a peaceful protest through charity. So even though your closing thoughts technically don't apply to me I still felt like I was being talked down to directly simply because I didn't like the ending. Considering the rest of the article had been articulate and temperate, the closing thoughts felt more like an angry, loaded rant than anything else. You let the beast out a little there, and it didn't do you any favors.
TL;DR (Since this turned into a wall of text anyway XD)
Overall opinion: Pretty good article, well-worded, I disagree with several points, and I feel like the overall point of the article got lost in itself. Instead of an explanation on why the endings were good, the article goes into a detailed analysis of "The ending makes sense because science" rather than "The ending was good because reasons."