1. Mining. Mining in general, mining in every way. Too many varieties of ore per field, awful respawn rate, mobs of a level inappropriate for the field, abysmal exp (fixing the spawn rate would probably fix the exp issue mostly).
2. Buffs in general. Disappearing or falling off after every gate, having to rebuff at every gate, randomly not seeing group bonuses (even though they're there).
3. Group frame bugs, especially after crashing and coming back in, the crashed person can't see the group frame until someone else leaves. Sometimes, player frame locations get jumbled up - for example, clicking on group member #1 would actually target group member #2, and vice versa. The hull status bar is particularly bad at updating - incapacitated group members will actually show full hull, I have to target them to find out if they're actually incapped or not.
4. Ammo stacking behavior and equipment swapping. You used to be able to swap items in warp UNLESS it was your engine you changed (which would pull you out of warp immediately). Moving stacks of ammo around from guns to inventory, inventory to guns, guns to other guns, sometimes ignores the quantity you actually select, and just moves the whole thing. Annoying when I'm trying to balance stacks of ammo. Annoying when I'm throwing in travel gear and the formation leader takes off before you've even finished. Equipping a roadrunner device while in warp used to retroactively increase your warp speed.
5. AUTOFIRE. Gets stuck, then unstucks, sometimes one gets stuck on autofire but isn't actually firing, etcetc...
6. (I know you said 5) MINING. And not just JEs! Us non-jenquai explorers love our downtime just as much as they do!