Okay, for the most part levelling from Ensign to Commander isn't that bad, still there is quite a few deep space missions you have to do in order to level, that'll quickly bore some people so either the XP for exploration missions needs to be increased or more PvE missions needs to be created to fill the gap, after your 100th deep space XP farming mission you'll start to realise that, unfortuntely this IS the game.
For the most part though, the missions that are offered even though they are cookie cutter missions, they are actually pretty fun to do, we just need more missions per-level instead of one or two, heck even if the reward was just a chunk of XP and Energy.
For the main issues though, I've singled out three main ones, one is still a crucial issue that needs to be fixed ASAP before it starts to do serious damage to the game, and I mean it - its a showstopper/deal breaker issue.
1) Fix the crystalline entity fleet action, prevent it from being able to receive 'ramming' or 'mine' damage, have it spawn in a random spot will not fix it, it'll just slow the energy farmers down slightly. All the energy credit spam is coming from players who are farming this, don't believe me - go there yourself and see.....in fact ban a few while your at it.
2) Alpha Centauri deep space mission, remove the spawn point camping Romulans, and remove the flight path of several groups of them that go close to the spawn point as well, nothing worse than entering the encounter to face of 2 groups of rommys, worse when they have flagships in the group too.
3) Psi Velorum deep space mission is bugged, nothing works in this encounter and needs to be fixed.
4) Exchange is still having issues, many items are not being displayed.
5) Breaking the planet has been bugged forever, maybe soon its time to fix it?
Fixing the ET is crucial, not only prevents it being farmed, it'll cut down on the gold farming spam too. Other than that, more missions needs to be available at all levels of the game. Whilst the PvE content is good, there simply isn't enough so you are forced into never-ending deep space grind fests which quickly get boring, having more missions and exploration missions that give better XP rewards will help.
What, exactly, is a Deep Space Mission? I'm Lt Commander 7 & not come across any yet.
Deep Space Encounter. When you get attacked by or attack an enemy contact in sector space. They are group missions where you need to kill a number of enemy squadrons. Currently Defend missions which involve completing 3 DSE's are the best XP/hour if you jump between instances and so avoid the five minute reset and especially if you hop into an almost completed instance.
Basically if you get to a point where you have no missions you are probably best to go run a level worth of Defend missions.