I think there are a couple reasons you don't see a lot of threads about MLB exclusivity, but there's one major one:
The news didn't affect this year's game.
I'd venture to say that if NFL2K6 were releasing with the license - basically, a more fully realized version of 2K5 - people would be a lot more satisfied and content that the game "had it's chance", so to speak, to be more fleshed out. If you look at MVP, it's about as solid a sports game as it gets. Other than presentation, there isn't a lot of room where people can see where MVP needs major improvement. NFL2K5 was a very exciting but also very flawed game that showed tons of promise. The frustration a lot of people feel is that the game was sort of cut at the knees before the potential it showed could be realized. Most people can see themselves playing MVP in the future with updated rosters, simply because there aren't a lot of improvements the game needs to satisfy most gamers that already love it.
MVP wasn't suddenly taken from it's fans; people were looking forward to MVP 2005 - not MVP 2006. Contrast that with people looking forward to NFL2K6, only to be forced with the reality of realizing the game will be changed drastically because it won't have the license. Or, that the possibility exists that VC may not release a football game at all. There's a dramatic difference between the two situations, and that's what adds even more fuel to the fire. And we don't need to add in EA's bull in a china shop approach to the way it does things rubbing people the wrong way also.
I don't think it's a stretch to say that if there were a NFL2K6, and it was as good as people were hoping it'd be, there would be a lot more people content with the situation.