These are all great. I could think of a bunch but my top would be:
1) Full roster mod snapshots
2) Character-to-character and character-to-inventory mod swapping from the mod management screen
3) Bookmarking feature for nodes with its own dedicated tab to simplify node farming
4) The ability to tab between selections in ANY and ALL contextual menus (units in a squad in GAC/TW, and DCs, for instance)
5) This probably deserves its own discussion entirely, but a complete overhaul of the officer/guild management and communication tools suite