The game I'm primarily drawing from was made in like 1995 or something, so it lacks a lot of modern conventions. I've noticed that crawler style games have more or less evolved into ARPGs. Having things like regenerating HP/MP has more mechanical complexity and build diversity, and allows for different builds and playstyles (eg cast from HP, drain HP on hit, etc).
Since I ultimately want to automate party exploration, sending out groups to grind dungeons means that if you're taking a long time to end fights, then fighting itself costs time, which means less resources/time, compared to a more optimized party. If things like logistics and seasons and time of day come into effect, then time becomes an important intangible to consider. When you're manually controlling a party, it wouldn't matter so much per se, but if you have say, a dozen groups going out, that's when it would matter more since it scales differently.
But that still doesn't quite address the issue of spamming defend commands and doing nothing to advance the fight. I think that I'm leaning towards having a sort of action/fatigue counter per encounter, eg every 25 turns, you lose 25% of your regeneration potential, so eventually you can't sustain yourself in a fight, assuming the monster you're fighting hasn't run away by then.
In-universe, I wanted to have magic take place via Leylines, but misaligned ley would leak magic into the world, via "Mist" (think FF). Over time, these regions change with the leylines, but concentrated mist can grow into crystals, so certain areas could have more corruption. But what I don't want to do is that "Oh you spent too long in the dungeon, you're corrupted and arbitrarily die!"