There's a fairly complete discussion of settings that block fictional players from starring but allow them as fill-ins and scrubs in
a recent thread.
I use two minor leagues (AAA for your potential ML players, AA to ensure my AAA team doesn't, say, run out of starters due to injuries, then burn up two kid pitchers by throwing them on one day's rest until they break down). DO NOT restrict your roster size at AA and just buy five spare starters and two extra backups at every position as minor-league FA. They're cannon fodder, so pick the worst, easiest-to-sign ones.
I set my amateur draft to take place about two weeks after the season and disallow trading of draft picks, as it's too easy to skin the AI on a trade (adding bad third- and fourth-round picks to convince it to throw in the first- or second-overall pick on a marginal trade, for instance).
For older leagues, I set the percent of foreign players down to about 3 percent.
I play every game, but auto-play to the top of the seventh and if it's lopsided, skip to the end of the game. If it's close, I manage it to the end from there (I think of it as the Jimmy Dugan system of management from "A League of Their Own.")
I do not equalize financials as the teams get too homogenous that way ... I like having big and small markets represented ... I'm currently playing the NY Giants and trying to keep the Yankees from taking over the city as a market in the 1930s and 40s (who cares if they have Lou Gehrig ... don't you want to pay to see Hughie Critz play? Slick Castleman? Gus Mancuso? The St. Louis Browns are also a good challenge ... as are the Washington Senators.)
Good luck.