Listing EVERY Player Who Did NOT Appear in MVP Baseball 2005 

That is due to them not playing in a single official MLB game up into that point. When they did roster updates back in the day they probably put them in. With the MLB the show series these days they have actually reached a point where they can use MILB players without the player having to appear in an official MLB game.

No shit

Kevin Millar and Shane Spencer are in an old MLB game. Can't remember which game it is, but I also saw Brian Daubach and Menechino in the game.

Because bonds was “out” of the game, ie “86” means a restaurant is out of an item

Yep! He was also in MVP Baseball 2003.

Bonds was in every official baseball game up until 2004.