The ability to disable enemy Instant Death attacks: These are not fun, even if they do provide danger. (This is especially true if you enable Death Real, where simply being unlucky would end your game.)

Experience growth rate, separate from Monster Difficulty. (The problem with the Monster Difficulty option as it stands is that stronger enemies give more experience, making the game easier rather than harder.)

Food consumption should have a zero option (maybe I don't want to deal with food this playthrough?).

Number of enemy types per level (the game would be more interesting if there were 3 or 4 common types of enemies rather than just 2).

Selectable level cap (maybe I want to deliberately limit my eventual power without making the early game harder).

Automatically identify items (some players don't like not knowing what their items are).

There's one problem with this argument; with food consumption at maximum, you use food much faster while awake than while asleep. (Also, Create Food/Water exists, making the food issue moot for Clerics, plus it's possible to find a Ring of Sustenance which eliminates food consumption entirely.) There actually is a major difference. In Elminage Gothic (and in Wizardry before it), you have a party of adventurers. If one goes down, you still have the rest of the party and can attempt to revive the fallen character. In Dungeon Hack, getting hit by instant death ends your game.

Also, a simple search on Google for "roguelike permadeath" yields the following article:
http://www.gamesetwatch.com/2011/01/column_play_rules_of_roguelike.php

The very first of those rules is the "no beheading rule", and I consider the Cockatrice enemy to be a violation of that rule, and therefore bad design for a solo game with permadeath.

Edit: There actually is one change I would make to Elminage Gothic if roguelike-stype permadeath were implemented: No random teleporting into rock. I believe the computer (not console) versions of the old Wizardry games would not allow a random teleport (whether via in-combat MALOR or a teleport trap) to teleport you into solid rock.

Clerics become less useless once they deplete their spells, so they need to rest.

Fighters/Thieves/Paladins, on other hand, can function without resting as long as their HP allow, so they minimize damage taken to increase efficiency. E.g., there are Death Knights who can hit for 80+ damage. Without food consumption, you could simply rest after each fight instead of trying to trick those Death Knights.

Food consumption could be eliminated while waking though, I agree. It adds to the pressure when you are not doing anything useful in game.

I'd add respawn as option too, which has several choices:
1. Totally off.
2. Turned on but only when you leave that dungeon level.
3+. Purely time-based (higher number = faster respawn).
And another option - maximum HP roll on level -up. In this game it is a MUST for melee characters or those Death Knights and similar monsters turn into another Instant-Death machines.

All I want is more ways to identify items. Otherwise I really like the old feel of the game, its rules and features.

Not an option, but a feature the game should have had: The option to call and name items.

Call would allow you to give a name to a type of item. For example, call Sapphire Rings "regeneration" (because I've observed one causing health to regenerate), and onyx rings (not sure if that exists, but you get the idea) "cursed" because I already equipped one and couldn't remove it without Remove Curse.

Name would allow you to give a name to a specific item. For instance, maybe this specific weapon works on enemies that require +2 weapons to hit, while this other identical-looking item does not.

Also, on drinking an unidentified potion that doesn't auto-identify, the player should be given the option to call it right then. (For example, potion gives you a warm feeling, so call it "warm".)

I know that Nethack lets you do this sort of thing.

This feature would make unidentified items more manageable for those who don't have Improved Identify or choose not to use that spell.