I agree with you on this point. I see it a lot in my RTTS where the team's supposed "bullpen anchor," set-up man, or closer is performing absolutely horrible (ex. "anchor" was a 1-3, 5.48 ERA and 7 BSV, set-up was 2-6, 6.92 and 8 BSV, and closer pulled a "Valverde" in either blowing 3-4 saves in a row or making the save but loading the bases or making it a 1-run game in the process) and there is no shuffling in the bullpen. I've seen managers in real life shuffle the order just to let struggling relievers work in a different situation (like the closer moving to a non-save opportunities or set-up to be more of a middle-inning reliever).
Also, I've seen it where my set-up reliever is moved into a spot-start when a starter has a day-to-day injury instead of using a long reliever or the extra starter some teams carry. In one RTTS, J.J. Putz started twice instead of using either Arroyo or Garland (both starters being used in long relief). In another RTTS, Junichi Tazawa is starting while Peavy is on the 15-day DL while there is a 6th starter in long relief.