You could try this:
http://www.planetootp.com/FakeHistory/Default.htm
These are the instructions to start a historical league (1901 in this example but you could use any year) and delete the players to create a fictional universe.
Or you could import any season from the Lahman and sim 50 years so that all you have is fictional players.
I believe that there is also a MLB template at PadresFan website that has all the logos, unis etc for a fake MLB universe.
Hope this helps....