My ideas for the hypothetical HexenRL (feel free to share your ideas):
Classes:
In DoomRL, the Classes in strict RPG terms are more like the three people who took the same class but invested in different skills, thus Marine is a sturdy soldier, the scout is an agile soldier and the techie is a smart soldier.
HexenRL should have more distinct classes, with very few-to-none shared advanced traits (or even basic ones if you go for extremes), exclusive equipment (The Mage will never lift a Fighter-only two-handed thunderhammer for example), different effects of common items like in the original game, same assembly recipes resulting in different things for different classes (Fighter: Steel Shaft + 2 Power mods = Halbert; Mage: Steel Shaft + 2 Power mods = Staff of Lighting) and so on.
Ammo:
Add Red Mana, to complete the RGB color theme with Blue and Green mana. Higher Tier weapons use two types of mana, while the Ultimate Three-Piece Weapons use all three.
Monsters:
As awesome as Hexen is, it lacks enemy variety compared to Doom 2. Importing monsters from both Heretic and Hexen 2 will provide that variety, in addition of adding extra variations of existing enemies,