Top 5:
1. Hacking - more choices, more AI responses, more integrated visually
2. Champions - more difficult choices (ship/module unlocks), more integrated mechanically (K unlocks etc.)
3. Armour +stats - more important (when damage isn't high enough to ignore it, lower minimum damage)
4. Hybrids - more types/roles, more surprises
5. FS (Higher if you add fun twists, like FS not being so friendly) - more detail, more choices, more events
That's my wishlist.