My biggest complaints are the aforementioned phenomenon of modern pitchers being able to be used effectively in a two man rotation for the entire postseason, and the ability for starting pitchers to "bank" innings and then start multiple games in a row at 100%. See crazystengel's thread in the SimLeague Baseball forum about starting Brian Bohanon 17 games in a row, most of them at 100%.
The crazy thing about being able to overuse SPs so much is that in my experience, RPs are treated to the opposite extreme. I'll rest a closer for the last few games of the regular season, use him in the regular season for fewer innings and pitches than RL, then he throws 10 pitches in game 1 of the playoffs and is less than 100% for game 2. Greg Maddux can start 4 games in a 7 game series, each at 100%, but Mariano Rivera is at less than 100% after throwing 1 inning after not pitching for 3 days? It's preposterous.
A less important, yet desirable (for me) change would be to allow closers to enter the game in the 7th inning. I could be wrong, but based on experience I believe that the current sim engine only considers bringing closers in for the 8th inning (unless there is no other eligible pitcher, perhaps). Guys like Goose Gossage used to enter games in the 7th inning and get saves often.