1.Proper error handling. Bad meshes, for example, shouldn't cause the game to crash (instead, the game should handle the error gracefully by disabling the mesh in question and replacing it with a placeholder). Bad mods shouldn't cause the game to crash. Instead, when a mod has an error, it should either be handled safely if possible or the mod should be disabled. "This program has stopped working and must be closed" indicates a lack of any error handling at all.

2.Model-view-controller architecture along with proper isolation of mods. Mods should be kept isolated and sandboxed. The game should immediately be able to discern what parts of a save game belong to which mod.

3.http://en.wikipedia.org/wiki/Diff. In most cases, it's trivially easy to merge leveled lists; why can't the game do it?

4.No more hard-coded strings. No more hard-coded skills. Everything should be controllable by the editor. Again, this goes back to number 2.

Yes.

Though, to be fair, I think (some) of this has more to do with the GameBryo engine than anything Bethesda did. Though error-handling could probably have been handled better.