
#1. Artifacts should be purposeful. Mercantile feels like a wasteful skill because of how valuable artifacts are. A non-axe user will simply sell that 5,000 gold axe and have plenty of gold. If you could give it to someone in exchange for a special benefit, it would open up more options and make mercantile more appealing. In ADOM, a popular roguelike, you have to give away 6 artifact weapons to access the ultra endings.
#2. Level 10 benefits to medicine and meditation. Like, a massive boost to health or fortify mana every few hundred turns. They aren't so appealing otherwise.
#3. A poison-air dungeon so toxic you can't even drink a potion before it's ruined. (inspired by the secret area you have to walk on fire to get to. Toxic resistance should get an area too). This would make the #2 skills, and many others, more interesting in an environment where you can't use potions. Magic-free areas might offer other challenges.
#4. Though associated with lesser RPGs, being able to redistribute skill points would be interesting. It's sort of like fast travel, a convenience for many players.
#5. Hidden endings, ultra hard uber bosses, etc. Eschalon II's increase in challenge over the first game was very welcome. Crank it up more for III, for veteran players.
#6. PLEASE make a fast mechanic for bashing. My high-strength warrior hauled around half a dozen clubs as "lockpicks", but it often took several minutes to get a door down. "Bash until weapon is worn" should be an option.
#7. Make a time-limited random maze or two to really give cartography some teeth. It's still soft. Time-limited quests are usually in poor taste, but not when they make a niche mechanic better.
#8. An explosives shop.

#9. Better tolerance for hands-free casting. Improving the weight limit is pointless now because it's always far too low.
#10. Forage-only ingredients.
#11. A timer to show you when your special recharges.