I had the feeling from the last two titles that Emergent (the company behind http://www.gamebryo.com/) had a lot to do with what we could or couldn't do to the game - for instance the god forsaken NIF format (the format of all the models in the game) that was proprietary, and other limitations of the construction set.
I really hope that modders have a finer grained control over how user input is captured. In Oblivion and Morrowind you mainly had ugly menus with buttons you had to click. I'm hoping that radial wheels and even temporary key rebinds are possible for mods (i.e. if you transform into a creature, different controls).
I think easier adding and changing of animations would be very exciting as well for most modders.