Here's a couple possible improvements that could be made to the game I'm currently playing, Stranger of Sword City Revisited:
* Allow the player to directly equip items from storage. (Saviors of Sapphire Wings allows this.)
* When there's a trapped chest, and the party's open locks character is able to eliminate all but one possible trap on the chest, you can either choose to disarm the trap (guaranteed if you choose the right trap, which is guaranteed since that's the only choice), use a Butterfly Arm (allows you to safely open the chest, pointless in this particular instance), or leave the chest. There's no option to open the chest and trigger the trap anyway, and there should be. (There are situations when one might want to deliberately trigger a Teleporter or Mimic trap.)

Secret of Mana: You know all those missing dungeons that were cut and the rest of the story? (It's clear that there's a few missing dungeons.) Put those back in.

Ascendancy: More lore, more robust victory conditions, more visual ship designs, better readouts of stats, higher rate of movement though warp.

Sims 3: Rebuild of game code to optimize and replace the launcher with something that isn't an awful Internet Explorer page.

Avernum Series: First person tours/collaborative work with Cyan Studios.

Simcity 2000 (SNES): A bit outside the norm, since this is more "fix a lame version of a favorite game", all I'd do is have it be remade by the Simcity (SNES) team or the SimEarth (SNES) team.

Knights & Merchants: Better priority management, better pathfinding, better battle management, streamlining & reduction of redundant buildings, better map scaling.

The Legend of Zelda: The Minish Cap: Kinstones are a waste of a button. I'm not sure what I'd replace it with, but I'm sure most of them could be completely eliminated, since they often lead redundantly to other kinstones or rupees. Also, give Link a mute button.

Cosmo's Cosmic Adventure: My kingdom for a smoother moving sprite, soundblaster sounds, maybe a better level curve, better camera lead, less gotchas.

"You cannot love something unless you can see its faults and be critical of it." Beautiful.

Dragon's Dogma: Dark Arisen (Some spoilers...)

» Modding support: This game is way too hard and troublesome to mod (pure hex and xml editing), and with it's convoluted development story it was rushed out and many things got out of the game... They should've made backups of the source code back then (Maybe they did? Who knows...) to facilitate modding through the years. If we had something like Skyrim levels of modding in it, Bethesda wouldn't be able to sell so many versions of Skyrim through the years because DDDA would take the market with it's epic mechanics.

» More/better enemy spaws, NewGame+ with high level enemies instead of re-used low level ones: Vanilla NG+ in Dragon's Dogma is a shame. (Again a result of rushed development). Many places in the vanilla world are empty and void of enemies and meaning. But the game does have many enemies variations and bosses that could (and can) be placed around the world for pure chaos and fun. (Specially post-Grigori mini-bosses/ mid-bosses and BBI enemies...).

» More loot, with better balancing: Many items/weapons/clothes, that are usefull, are hard to get, requiring repetition in mid-high level and secret areas. This could be solved if they added more itens to the world, or variations of same itens with different stats and effects, as the game already have a toolset of mechanics that contribute to this scenario working. Ex. that could work: A Fire sword (primary element: Fire), could also be Thunder element (secondary element: Thunder), with different stats, but still weaker in Thunder than a Thunder sword (primary element: Thunder), (secondary element: Dark) weaker in Dark element than a primary element Dark Sword - and so on.
This style of weapon/itens/clothes stats would use DDDA elemental/environmental mechanics to it's best imo.

» Same as above - but with enemies.

The same could be said of Ultima 5 (NES): Have it be remade by the team that did Ultima 4 (NES). (Ultima 4 (NES) is a good game, even if not that faithful to the original; Ultima 5 (NES), on the other hand, is not.) Alternatively, make the game for the SNES instead, using the engine used for Ultima 6 (SNES). (Or just make a more straightforward port of the Apple 2 verison.)

Ultima 4 (NES):
* Restore the dungeon hallway events that were in the original, which means putting things like barriers and dungeon traps. (Some modifications would be in order, however, like not having protection fields that block your path unless dispelled.)
* Restore the removed dungeon rooms. (Some of the dungeon rooms from the original were removed; in their place are rooms that are duplicates of other rooms.)
* Restore the NPCs that were removed from the English version (but were present in the Japanese version); also, where it makes sense, use the original lines from the PC version instead of translating the Japanese. (Some changes may need to be made, of course, like making sure the dialog still says most of the horses have been eaten.)
* Make it easier to get money. (Money is a lot harder to come by in this version.) Also, reduce the price of the Key sold at guilds. (The key here has infinite uses, but costs 2000 gold, which takes a while to get, and it's a required item.)
* Make "AUTO" not the default command during battles, and also make the "AUTO" command never cast Missile (wasting reagents). (Or, alternatively, make the Missile spell not require reagents. After all, it's weaker than Fire, which needs the same reagents to cast.)

Well, I doubt they will release any source code. Let’s hope that OpenMW comes on, it works great for MW now, so hopefully once it becomes 1.0 then focus can be shed on oblivion.

Mount and Blade : Towns and cities should appear more prosperous when you visit them, as they grow more prosperous. And if you build something like a mill in a town you own, then that mill should be visitable, or at least viewable in the town.
I don't know if bannerlord perhaps does this.

Civilization IV
* Rebalance the effects that vassals (particularly peace vassals) have on diplomacy. Make easier for vassals to (re)gain independence.
* Give an improved effect to the serfdom civic so it's actually useful.
* Rework how the Apostolic Palace works so its decisions don't drag civs where its religion is barely present.

As someone who played the Morrowind and Oblivion with planned leveling, I can confirm that it can be quite annoying and boring. Indeed, you can see Bethesda attempting to correct aspects of the leveling from Morrowind in Oblivion (like not being able to train a lot per level) and overcorrecting it in Skyrim, removing stats altogether.

Personally, I like the lack of caps for the stats. Drinking potions until they become ridiculously high is very much part of the fun to me.
Yeah, I know. It would be beneficial to Oblivion (and Arena) more than anything else. As you said, OpenMW is already awesome, and Daggerfall Unity is pretty awesome as well. I never understood why nobody tried to do something similar for Oblivion. I guess it's too middle of the road between Morrowind and Skyrim and people tend to gravitate towards one of these other two.

Kenshi: More weapons, clothing, and armor. More AI companions that are customizable the moment you recruit them. More bounties, and just the existence of quests. Rideable animals. And lastly, better optimization.

This actually reminds me of something that's always bothered me about the Civilization games; the fact that Monotheism is an advance that requires Polytheism. Essentially, the developers are sending the message that Monotheism is better than Polytheism, and I don't like that.

A better approach would be to simply give these advances different names, perhaps "Religion" and "Organized Religion", and avoid specifying what sort of religion these two advances are referring to.

Great game and good idea.

Like I said. I love it. But Kinstones are just sidequests done wrong.

Adding another one I already said in another thread what I'd change for: Arcanum:
- If a companion's level is below the PC's level when they join, level them up to match, seeing as companions level when the PC does and if they're below, they'll forever remain below.
- Let companions learn from schematics too.
- Grant combat experience in a way that doesn't force the PC to be a character that can hit enemies lots of times. The regular per kill way, or if you want per hit then make it so a hit from any party character counts the same, or maybe grant it per damage dealt, again by any party character.
- Do something about those terribly tedious Black Mountain Clan Mines...
(That's on top of bugfixes, of course.)

That's still not good, as it means that pure support/healing builds don't get any experience. (See Disgaea 1 for an example of where it's an issue; the only way to get XP is to inflict a killing blow, which means healers don't have a reasonable way of getting XP. Well, except for the clear bonus, but that's not a particularly effective way to reach decent levels.)