just do the research on years and how many teams were added, etc...
edit league structure during those years to manually expand. the automated stuff won't do what you want to do.
as far as the nhl/nfl, i'm not sure why they are confused. pretty sure other people have done similar things in the forums -- just teams/nicknames/cities.. he isn't going to expect them to play football on a baseball field in a video game. LoL
although, if you are, that's not possible
historical play will expand the MLB as it did in history... since it's not a nfl/nfl game tehy don't have that history in the game, unfortunately, so yes all manual expansion for any sort of thing that isnt' mlb baseball history.