If you are serious about fantasy baseball then you are correct, this would not work. My friends and I love baseball, but have only played fantasy baseball with very casual interest-- i.e. usually we draft teams, maybe throw $5 in each, then no one checks their team very much after that.
This is just our way to do something new, and an excuse to do something with baseball cards-- the object is basically to set it and forget it. If you buy a Topps cheap-o set, you'll get all the players and I believe no dups. If you draw all relief pitchers, then yeah that blows for you. But like I said, this is just an excuse to have some fun with cards. The actual playing out of the season will be a footnote. The only roster moves allowed are trades-- we're not the type of fantasy baseball players to maintain rosters throughout the season. I call it the "Ronco" Rotisserie league (set it and forget it).
And I'll fully admit that it could be terrible and no fun at all. However, I am hoping to find a site with larger roster sizes. So far the largest I've found is 40 on ESPN. If anyone has any better suggestions let me know.