Looking back, I think it's really strange that FTL made enough of an impression that the GB staff all felt like they should get around to playing it leading up to Game of the Year (and some of them actually did), while I'm not sure The Binding of Isaac was ever mentioned again after its Quick Look.
I don't know if others thought of it this way, but FTL has basically been this year's Binding of Isaac for me, as far as being a fairly tough roguelike-like thing that tasks you with playing it multiple times to unlock all the stuff, and you never quite have the same permutation of things twice. I really like both games, but I actually think Binding of Isaac is the better game. The major flaws of FTL are 1) with a percentage-based dodge rate, sometimes you get unlucky and just get ravaged by missiles even though your ship is pretty good, and 2) while every ship starts with different stuff, if you manage to reach the boss, your ships kinda all play the same because you can always just upgrade shields, engines, etc. how you prefer every time (weapons and drones are more random, though there aren't THAT many). Conversely, The Binding of Isaac gives you direct control so you can theoretically tough it out and dodge like a fiend even when you are severely underpowered, and there is no upgrade tree you feed money into so your stats and items are wildly different each time (and there are like a zillion items).
Granted, the text adventurey part of FTL is really neat, and its setting is more engaging than Binding of Isaac (which apparently is meant to express McMillen's thoughts on Christianity, but all I've been able to figure out is "he thinks Christianity is kinda stupid and goofy"). Anyway, I think both games are comparable to Spelunky, so I just don't really get why FTL and Spelunky seemed to get far more attention than The Binding of Isaac ever did last year.