How would you suggest "fixing" this, without causing other issues? Establishing a minimum # of pitches (say 25) a RP could throw would create a whole new super class of closers, guys who in the past 8-10 RL seasons were righty or (most often) lefty specialists. Should Joe Thatcher (.54 IP/G, 0.86 whip, 35 IP/162) really be able to pitch to five batters, when he commonly was used to face one or two lefties? Had he been used as a traditional reliever and faced more righties, his numbers would have been less stellar. There are some pitchers who are hurt in the sim because of their effectiveness, such as the 90 Eck who rarely faced more than four overmatched hitters. But the engine is set up to based # of pitches on IP/G, and any change would also have an effect on appearance fatigue. If you start tinkering with those, the unintended consequences could be huge. Would upping Eck's pitch-count ability reduce his ability to bounce back to 100%? If so, someone like Thatcher cold never be used the way he was in real life, to frequently come in to face a couple of lefties. Would doing that make Milacki unusable because of appearance fatigue? If you didn't also adjust appearance fatigue and simply allowed pitchers to throw more pitches per appearance, all the cost calculations to figure salaries would have to be revised.
I understand the frustration with RP like Eck being unable to pitch an inning against stacked lineups, but any solution to that is likely to cause greater problems and loopholes. The easiest fix to this particular problem is to only play in low-cap leagues that have more-realistic lineups.