Wishlist? Aight.
*Better map generator. Current DoomRL maps tend to look very artificial, would like to see more organic dungeon layout (not every level being a perfect rectangle consisting of square rooms with 1-tile walls etc). I'm a big fan of how Brogue does this (randomized enviroments together with heavily scripted key vaults/traps scattered about) - having, say, premade alcoves opening up to reveal monsters as the player approaches would be very doomish and neat. As would implementing keycards and switches changing the dungeon layout that the player would need to find in order to proceed.
*Cover system, eg standing behind a piece of furniture or at a corner would give bonus armor versus ballistic attacks from the obvious directions. Clear visual cues showing the player which monsters he's currently in cover from.
*Mutual LOS. Yeah, not that big a fan of cornershooting. Also functionally infinite LOS range but for blocking terrain and terrain features. If the LOS range is artificially reduced, there needs to be a proper explanation for this, eg smokescreens or local light conditions.
*Slow projectile weapons to compensate for the lack of cornershooting, meaning plasmaballs behave as charging lost souls do currently. Obviously the map generator would need to take this into account in order to spawn enough enemies and wide enough spaces in order to make dodging everything difficult to impossible. Also would require enemies utilizing these kind of weapons to downright refuse to charge the player single file down corridors. To compensate, projectile weapons would ignore (and sometimes destroy) cover. This would mean the player has the dual compunctions of seeking cover to shield himself from ballistic weapons and staying mobile to dodge projectiles. Add keeping distance from melee enemies and that's quite a lot of priorities for the player to juggle right there.
*Better AI. I mean it doesn't need to be at Smart Kobolds level but even little things like staying in cover relative the player, (sometimes) sidestepping projectiles and avoiding bottlenecks would at least require us to find new exploits.
*Renaming damage cathegories. I mean Plasma contains more thermal energy than fire by definition, and it isn't like missiles destroys stuff by setting them aflame. One could probably also collapse the current fire (or concussive/explosive/whateveryoucallit), melee and ballistic damage into one type since they all boil down to kinetic force. Corrosive damage still work as a unique type I suppose, as do radiation sources and electricity (granted they eventually boil down to thermal energy as well, but the mode of delivery is still unique).
*Player progression and later enemies being defined by new abilities rather than bigger numbers.
*Non-directional audio cues. being able to deduce direction of sound on the X-axis is weird and immersion-breaking to me, and knowing that something is close by but not where is scarier anyhow.
EDIT: Oh yeah, and just so that I don't only rehash my gripes with DoomRL, what about replacing any potential food system with the main character being addicted to combat drugs? The player has to keep him above a minimum threshold or face lower performance out of his hellguy, and eventually go into abstinence (not killing the character outright, but crippling his stats across the board and inducing hallucinations and epileptic fits). Willfully overdosing the drugs would also be an option, temporarily raising stats at the cost of washing the excess drugs out of the system faster.