If you are looking at doing a league using MLB teams but filled with fictional players, I suggest you look at these two threads:
STADIUMS
UNIFORMS
They tell you exactly when to use which graphics.
If you are looking at creating an entirely fictional universe I recommend you find the unis and logos you like then name your teams after them and use them in-game.
This guy's unis are my pick, but spend some time on the mods board picking them off - the possibilities are almost endless. Same goes with stadiums.
If the idea of full fictional does your head in then I suggest you consider the import historical rookies option, which will give you some familiar names among all of the AI-generated ones.