First of all, Baseball games are not the premier sports franchise in video games. In 2004 baseball titles took in $93 million while football games took in $384 million. I know that basketball games are somewhere in the middle and I'm guessing that soccer's world-wide popularity also puts it in the middle making baseball at least number 4 in video game sports.
Secondly, Take-Two's deal only precludes third-party publishers from using player's names. That means that Sony's, Nintendo's, and Microsoft's internal studios are not affected.
Thirdly, the deal is only for player's names and likenesses. The team names, ball parks, and other assets are still useable. And, let's remember that Barry Bonds is not a member of the MLBPA, so he could be the cover of a rival game.
Fourthly, Take-Two is rumored to have spent between $70 and $150 million on the deal and it didn't even get them ballparks or exclusivity from first-party publishers. That seems like an awfully big price tag for a genre (every baseball game out there) that only pulled in $93 million in 2004.
Fifthly (is there such a thing), Take-Two has been and seems to want to stay a one trick pony. That one trick is the Grand Theft Auto franchise. At least Take-Two already has the graphics engine for swinging a baseball bat. By making this seemingly misguided deal, Take-Two proves that it is willing to swing at pitches outside the strike zone.
For more information, check out the CNN/Money article.
Also, in a related story, SEGA has sold off its in-house sports studio, Visual Concepts, to Take-Two for a reported cost of $24 million. Take-Two has recently been the distributer for ESPN/SEGA games such as NFL 2K5, etc. After the EA and ESPN deal was announced, that went out the window.