You can play multiple seasons in League mode, but there is no relegation/promotion. Also if previous Pro Evos are anything to go by, any changes you make to team rosters and lineups in the main menu should also apply to teams in League mode too, so you can effectively make up your own transfers in between each season (might be an idea if you find the ML transfers unrealistic).
ML has domestic cups in it, but they are still separated into D1 Cup and D2 Cup for some stupid reason.