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Okay, so Hexen, but with the Hexen 64 lore blocks upon entering a level, a variety of over-time monster spawns depending on the level, and balance changes so the three classes are more equal by end-game. Also make Korax actually difficult. Go!
I've had the idea and may still get to do such a spit-shined version of Hexen, but I'm also supposed to finish up Doomvengers for final release AND prep Heretic: Element Storm AND I've got that whole novel-publishing stuff to worry about soooooo we'll see.
I'm curious to see what tweaks you come up with. Personally, I think Hexen is polished, it just doesn't have the well-roundedness to expand its gameplay beyond the context of the original campaign. I think that to make the game moddable, you'd have to completely redo the weapons, monsters, items, and mana system. The changes you're planning sound worthwhile, though, so best of luck!
I've never played Hexen 64, so out of curiosity, what do you mean by "lore blocks"?
I think it's polished but suffers some balance issues - I mean by late game the mage is untouchable and the Cleric is much better then the Fighter. Only the Cleric's flechettes are REALLY useful, and bosses beside the Heresiarch are way too easy. Also I was thinking of somewhat more specific hints for puzzles, especially for the famously tedious Seven Portals.
In Hexen 64 there were loading screens that told you the lore behind each level. It was SUPER cool and really added to the experience.