The only problem I really have with Brad having ME3 as his personal pick is where in his top 10 he compares it being his top pick to the Academy Awards and RotK in terms of rewarding the trilogy. Considering that ME2 is probably in the top 5 or so most lauded-games of this console generation that's unwarranted, and your personal top 10 Games list shouldn't be to reward franchises. I fucking loved Assassins Creed 2 and Brotherhood, should I have placed Revelations at the top of my list that year even though it wasn't as great? What the fuck. I doubt that's exactly how he meant it, but hearing that really, really, really rubs me the wrong way. He justified his pick in the description up to that point, he didn't need to try to make excuses for it. Anyone who is going to give him shit for that pick was going to do so regardless.
In terms of the site's overall GOTY, it's largely irrelevant because we already know ME3 wasn't their pick. But it wouldn't necessarily be invalid either; I don't think it's necessarily come up a lot in previous years (at least off the top of my head), but I'm not sure there's a clearly divided line on most sites as to whether or not a game has to be considered only in it's at-launch/vanilla state or not for GOTY awards. ME3 is a bit of an outlier since as an RPG, further DLC isn't largely going to change people's opinions of the game one way or the other, especially as the "final" entry in the series (since ME2 was the middle chapter, DLC worked differently in a post-game sense). But then you also have situations with other types of games like say Diablo 3, which is a substantially better game right now than it was at release. So if a site is willing to consider the game in it's current state and not when it came out (accounting for patches, DLC, etc) ME3 is a completely valid choice.
Also Frog Fractions on this top 10 list is pretty hilarious. I'm not sure it would be on mine, but it does seem a bit out of left-field. I don't remember them talking about it much on the Bombcast. It is awesome though and everyone should play it.