Okay, so I'm going to admit first and foremost, that I didn't read your entire post. Because the second you said that people don't like the endings because we don't understand them, your entire post takes on a pretentious undertone, and that statement is completely superfluous. An appropriate opening would be "people dislike the ending, I think it's good. This is why..." Suggesting that the only reason we dislike it is because we don't understand is supremely arrogant, and I don't care what your qualifications are, it shouldn't be there. I have no desire to read something by someone who thinks so highly of themselves, and so lowly of me, and anyone else who shares my opinion.
However, I did read your section on "entropy", because I read Yahtzee's article as well, and this point makes no fucking sense. For one, "order" and "chaos" are really only mentioned when talking to reapers, and really only in the third game, post-rannoch. So that is less than one sixth of the entire series that actually mentions or alludes to it in any way. That does not qualify for a "main theme".
Furthermore, if one was to take "entropy" as a main theme, especially with regards to inevitability of events, then logic demands that the reapers should lose. Take into account the fact that reapers are supposed to represent order, and organics chaos. Now ask yourself a question. Does order increase in a closed system? Why no it doesn't. Does entropy stay the same in a closed system, representing the maintenance of a status quo? Why no it doesn't. Entropy always increases, and thus is layman's terms, chaos increases.
So if "entropy" is a main theme as you suggest, it contradicts your point within it, where you state that "the reapers always win".
You may also notice that this post is a little condescending, and you may be right. It's one thing to open a discussion with a holier-than-thou attitude, while dismissing your opposition's position because if they don't agree with you, then they must not understand, but it's another thing to do all that with fucking stupid arguments that are self contradictory.