My top 5 issues.
1. Broken (HU) missions. playing a progen I feel like I am being punished with these 30 stage missions taking well over 3 hours to complete. The missions are well thought out, and are very similar to what was in live, but the lvl 100 one... thats a whole different animal, because it has been broken in ST2 and ST3(not to it yet in ST4), because 1 specific mob just wouldnt continue to spawn properly. If it wasn't for the broken part of the mission it would be a welcome break to the monotony of grinding.
2. Eventhough i havent played a seeker, nor plan on doing so, this is still a priority over content "bugs". The classes should be worked out before the end of the final alpha test.
3. Finalize new classes' skills, I know the PP needs tweaking, and I am sure the others do as well.
4. Next would be the controller, and other end game raid content. These can be tweaked during the downtime between testing, and live, as they will not be applicable in the 1st 2 weeks of live anyhow. with the end game raid stuff, implementing "mob group agro" and increasing the speed of minions/adds to where they cant be kited would solve most of the issues.
5. Minor Annoyance is the activated skill graphical problem.. when you activate a skill that has a graphic, oftentimes it will stick and continually do it, now with enrage it just looks cool, like your ship is radiating an evil red aura, but shield charge/sap and grav link do this quite a bit.
6. Droprates from regular mobs seem a bit high on premium items, while drops from special mobs are way low.