This is probably all in the "obvious" category, but I thought I'd write it out in an organized way:
1. Filters that remove display of various categories of stuff, like hiding ships but showing stations, to make navigation to stations straightforward.
2. Smarter click-through checks; if I click on a fleet but there's a station underneath it, it should probably default to the station, not the fleet, as my target, unless I've done so in the Near-Space Display (my made-up term for what you see when your fleet's flying around, as opposed to the larger map display).
3. Filters by faction.
4. Filters that will show, with arrows, projected courses of the fleets in the system.
5. A long-range scanning device that will give us a prediction of fleet compositions. I'd also like to see strategic-level ECM and "stealthy" fleets that cannot be detected until close to a player, and ECCM to defeat same.
6. UI access to the Factions, their lore and relationships with one another.