Chiming in to say that a lot of things that make sense in the D&D rule book don't really make sense in a computer game, where modern gamers expect the game itself to tell them when something won't work, is out of range, or will have a negative effect.
First and foremost,
Cancel Action needs to go. Yes, it sort of makes sense playing a real-time game where decisions need to be made quickly so the the next player can get their turn, but there is absolutely no place for that in a modern single-player computer game, especially one that provides you so little information as to whether a particular skill/spell will do what you want it to.
Unless it triggers damage, an event, interaction, or requires a dice roll, EVERY action should be reversible, with no loss of action penalty.... even including movement.
Touch/Short/Medium/Long Ranges should be clearly visible graphically. Ideally, this should be something that pops up when an action is selected but before you pull the trigger, so to speak, but if that's too difficult, then having a player-centered HUD grid (that can be turned on and off) would be the next best thing. This, combined with the take any action back as long as it didn't trigger something rule, would make the game about 200% more user friendly for people who just want to play a game, but haven't memorized the complete 3.5 D&D rule set.
Automatic autosaves at key plot junctions or points where the party is likely to get massacred if they make the wrong decision. This is something that should be part of the editor as well. Case in point would be when deciding whether to burst through the first door or right before walking into the room with the virgin sacrifice, getting the bird guy to drop you off on the other side of the chasm, etc.
EDIT: Literally just ran into the first of these in the very next room. But there should be way more of them.
It is very easy to completely bone yourself and get into a situation from which there is no possible escape. A good example is the bit right after the moon phase tombs (which was brutally difficult, and I eventually had to cheat and add a camp fire with the editor, since all my characters had multiple stat drains and no means of erasing them) where you have to split your party, sending two up a ladder into the fire cave and the rest stay down below and fight a cursory battle. I sent my drake Storm Warrior and human Death-knight, arguably my two most powerful melee fighters up the ladder, but they got massacred *EVERY* time. A wizard or cleric armed with ice spells might have stood a chance, but because I was stuck and didn't feel like going back and having to fight all 6 tomb guardians over again, I had to cheat with the game editor and spawn some fire protective gear, because my melee characters simply got grappled and murdered in a couple of hits. (I can't even imagine going into that fight if I hadn't spawned the camp fire and repaired my stat drains.) Additionally, just a UI thing, but
when you hit the Escape key, that screen should pause all background music/ambient sound and bring up four options for Save/Restore/Main Menu/Quit. Almost every modern computer game uses Escape as the default "Pause" screen, for both muting the game for a moment and save/restore functions. Nothing against the file menu, but every time I get 4 bad rolls in a row and need to restart, I instinctively hit the Escape key, then have to remember it's File --> Load Game to access the save/restore commands.
There should be a Y/N confirmation before stepping onto a known damage square. Yes, the mouse-over does tell you to expect damage, but when move/interact are the same button an extra bit of confirmation can be nice.
Friendly fire... I'm totally cool with. It makes sense, and it warns you ahead of time (and the same rule applies to monsters) The only recommendation I'd make is including a red highlight or little friendly fire damage icon on friendly targets while determining the travel path of your ranged weapon/spell.
The chance to select pre-game starting equipment would be nice, but I'd be happy to have my starting crew pre-equipped with a wider variety of low-tier equipment based off their class/weapon/armor proficiencies. (Honestly, who goes into the dungeon without so much as a pair of shoes or a single healing potion?) This can be somewhat randomized or partially based on stats. (ex: Wizards and Clerics get between 1 to 1d6 random starting scrolls scaled on their Wisdom, Charisma can dictates starting cash and the quality of certain items, etc.)
Finally, lower level encounters should definitely dial back on the monsters' propensity for using overpowered area-effect spells like web, fireball, and stinking cloud.
I believe this is more-or-less built into the editor, but it's definitely something that needs to be addressed in the starting campaign, where the players' magic users start out woefully underpowered, but the enemies can wipe out your entire team in a single round before your melee fighters can even cross the room to get close enough to attack them.