Well, basically, the hard part would be making a GUI that can handle this. Actually I am very slowly working on my own game in my spare time, and this has been one of my goals from the start and it's going pretty well. Why? Well, just look at a game like morrowind or oblivion. Those games have a lot of people modding them. Unfortunately, no matter what you do, you still have a largely poorly done stat system. This also kills things in case someone wants to do a d20 star wars version that follows stats well, or wants a gurps system, or whatever.
Being able to put in a spell system/force system/superpower system is nice as well. If you can determine how the stat system works you can make any sort of game you want and seriously change the way gameplay works.
It would also be nice if there were ways to tweak the AI. Such as setting percent chance of charging/fleeing/fight radius, etc - whatever is available, for each unit. That way you can get behavior that makes sense for your newly edited world.
I don't think these things are actually that difficult, they just require slightly more thought and more software engineering towards the general case of things instead of just hacking out and getting it done. It takes slightly more work, but makes things that are near impossible to mod otherwise simple.
As for modding stuff as a suggestion all the time, that is a bad idea. Mods should NOT be game fixes. The reason why is that mods take a ton of effort, and if someone were to do this mod then very likely wen .801 or whatever comes out then it would totally negate all of that hard work.
There are still tweaks needed, but the combat is overall extremely well balanced; anybody will see flaws in any AI given enough time and perceptive ability. I don't think the AI needs a huge overhaul, and stuff such as having the ablity to retreat or a command to *truly* hold your ground would go a huge distance towards fixing the problems.
When I say largely complete, that does not mean there will not be changes, but the engine is very playable and useable, the game however, is not. The game is just roaming around fighting with no end in sight, right now. Some kind of scorekeeping or awards of land and titles would help, and maybe some factional stuff like in the last days mod. For example if you just sieged an enemy city for weeks (or perhaps defend your friendly army of besiegers) then it would eventually take that city over.