well the templates are usualy straight forward, so using a capital ship template (wich shows all the possible things to put in a certian field) would be nice, as well as things like weapon types (have a list of all the weapon types, animations, textures, sounds) which would prevent endless hours of searching through files. also the ability to add your own meshes/effects to the program would be nice too. abilitys would be way too complicated at the moment i would think, but if you want to spend hours learning all the possible uses for certian modifyes (which would take a LONG time, not to mention the templates verry a lot). research is usualy straight forward on the other hand and would be nice, expecialy something that can check the other files and locations of other research effects (every research subject has a location box, something to let you know if there is something currently in that slot would be nice) . also if you could add things like planet templates, frigate/cruiser templates, as well as planet modual (structures) templates it would be nice. mind you, this would take a lot of time and feedback from most of the community moders (from thoes doing particle/visual effects for some parts, to thoes who are heavy into coding). 

Another decent feature would be a section with moding tutorials, where certian things are explained in detail (like certian limitations, step by step instructions on how to do something, etc)