Depending on various circumstances, the PCL was an outlaw league at times. Reserved MLB players were blacklisted if they signed contracts with teams out west, but were probably just as easily whisked away from the PCL whenever MLB teams needed the talent. The PCL was able to free itself from the annual major league draft (Rule V I think) for a number of years, but I'm not sure if that prohibited them from plucking players at lower classifications. The MLB probably, at times, farmed players in the PCL, and the PCL farmed players in other minors, but team affiliations weren't really as widespread as between MLB and other leagues.
Some options include:
1) Increasing service time needed before becoming a free agent - This will keep young players around longer but will also not allow them to sign MLB contracts at a young age. Dimaggio played 3 full seasons in the PCL (18-20 y.o.). He was actually traded at the end of his 2nd year to the Yankees but on condition he spend another year with the Seals. So allowing trades between leagues is an option. Of course there were other stars in the PCL that played their entire careers there, and being paid year-round was an attractive incentive to stay and forgo a career in the majors, which paid less either overall or only during the season, and not to mention the nicer weather. Some would argue these players could well have starred in the majors.
2) Set up the PCL in another country by using one of the available "Nation mods" out there or by making your own. Then you can set foreigner limits for either league so as to allow some foreigners (easterners if you will) into the league. This will also enter the "home-country" advantage some players look for when signing contracts. To some extent one would have to believe the PCL drew from local talent (California, the NW, etc). Given history, MLB is probably more restrictive as to who they let into the league, even though they sought out to grab the best available talent.
3) Dr. Arbiter's post may give some idea
here. I haven't tried this myself yet, even though he's dealing with real players.
4) There may not be a very good and easy way to do all this without significant changes in the game's features. Reserve rosters become a problem without any limits and those may have to be trimmed manually from time to time.