I whish units data, models, textures and animations will be easily accessible with commonly readable formats.
I whish custom maps to be saved in an human-readable format (json, xml, whatever) for better control and manual modification.
I whish triggers to internally work on a c-like scripting engine (not lua for god’s sake, something like AngelScript would be heavenly, or ChaiScript, not sure about Javascript), i whish the editor user would have the option of adding triggers as raw scripts in addition to the old clicky, tedious and limited triggers interfaces.
Finally, i whish the test mode from the scenario editor to offer an ingame console that supports scripting on the fly for experimenting.
Please, make me happy 
Sincerely,
an AoM fanboy