You can throw in the ESPN license there too. They went from being called ESPN Video Games to losing it all. Whether you like Sega Sports, ESPN VG, 2K Sports or not, by the time 2004-2005 rolled around, they had set themselves up to be a very valuable alternative to EA Sports. Several licensing agreements really crippled them.
When you look at a potential EA license with the MLB, I'm sure Take Two thought that it was the best business decision, but the development of MLB 2K has not been parallel with that gutsy decision, not to mention the door being open for a first party to develop. It would be interesting to know why there was that stipulation in the contract.
I would agree too that 2K's baseball offering is along the lines of EA's football. This is the first season I'm still playing Madden after October. Still, I tried real hard last year to keep it going with MLB 2K9, but there were just too many issues that prevented me from doing so. That's where the exclusive deals are so different. Madden doesn't have an annual game challenging it, MLB 2K does and they are paying the price.