Bandit Kings of Ancient China (NES)
Revert the heroes name back to its original name instead of nicknames (For example: Nine Dragons should be Shi Jin).
Romance of the Three Kingdoms II
Make unplayable rulers (Kong Rong, Liu Yong, Wang Lang, etc) back playable.
Those should be easy enough to do if you understand the game's scripting language. I'd do it, but I have a backlog of projects already at the moment. I've done a lot of work on the SNES version of ROTK2. I made a modification of bsnes-plus that automatically would interpret the script and output it to a text file while the game was running. Here's an example of the output:https://www.dropbox.com/s/889nbq80ajr2ytj/ROTK2_script_wLabels.txt?dl=0
Script starts around hex x8000, you can get an idea of what the language looks like from this. Koei used the same scripting language for all their NES games that I've tested. The only SNES games that used it were ROTK2 and Gemfire, games that were made for both systems. Obviously it's a little different under the hood for the NES (the stack management is different), but the effect of the script commands is essentially the same. You can track the scripting in FCEUX by keeping tabs on reads from $06, which holds a pointer to the script command or operand currently being executed. In the SNES version, $04 held a pointer to a location in the stack, used to keep track of arguments and local variables available to the current script function.
A huge amount of the logic in these games was scripted. Unfortunately, I don't have a similar tool for the NES, so interpreting the script has to be done by hand for now.