In the real world ordinary relief pitchers often have ERAs a run lower than average.  Really good relievers are often two or more runs better in ERA.  Of course that's because they can put everything they have into every pitch for a few batters per game.  Believe pitchers with lower stamina should  have higher, in some cases much higher, ratings in other categories.
While you're at it, get rid of the really low stamina pitchers.  Even though some relievers are routinely used for a batter or two, there is no healthy professional pitcher who can't throw at least 15 to 20 pitches per game. 

I'm not sure what you mean. They have all kinds of RP in HBD. Good, the bad and the ugly. Really good, really bad and really ugly. And I never set a PC lower than 15 pitches, even the low stamina guys. They can go that long.

It's owner usage.   If we have a RP with splits in the upper 80s and two pitches between 85-90, we set their pull at 1.   So, if he walks a guy, gives up a homer and two more hits, he gets pulled.  Then, if the next pitcher gives up those two runs, you've got a pitcher with 2/3 IP, 4 ER.    If he only throws 50 innings, that's .72 change in his season ERA. Change your pull rating and watch the ERA for your RP go down.