Sega/Blue SHIFT *is* Take Two (cf this post from a month ago:
http://www.gamespot.com/ps2/sports/espnmajorleaguebaseball2k5/news_6114690.html) ...I hope you like cross-hairs in your pitching interface. LOCK ON! LOCK ON!
Your confusion with the exclusivity comes stems from missing the key words "third-party". ("Beginning in 2006, Take2 will have exclusive rights among
third-party publishers") "First Party" is industry lingo for the console makers themselves. ("Second party", btw, is a out-of-house team that works exlusively for a first party developer (eg, Retro for Nintendo))
And the MLBPA is most definately not the MLB with a couple more letters. They are their own entity and operate within their own bounds. The MLB will probably ink the same deal as the PA did, but only because they realize splitting the brand is a rediculous move for all involved.
Look at it this way - FIFA (the EA game) got exclusivity from FIFA (the football org) and what happened? Pro Evo kicked their ass. Maybe we'll see a serious upheaval in both the american football and baseball markets as well.
(Silver lining, etc)