This is a big wall of text, but please read all of it to get the full idea.
Balance is very hard to ever get right as no one can agree on what powers need buffing/nerfing etc. No matter how much something is tweaked, there will always be debates.
The fact we also have a very large number of abilities now means that its getting very messy inside PvP maps with an array of different things hitting you at anyone time.
So my idea (which is quite drastic) would be a PvP set up that is separate to your PvE set up. This would only need to affect Space.
There is a screen like our normal ship boff station set up but its radically different. We only get to use a smaller number of boff powers. It could be as simple as everyone gets one ensign power for science, tac and eng, and one lt. power to match their ship class, but thats just a rough idea.
Everyone can still equip the same number of weapons, and get their inherent powers but the higher level ones, like miracle worker, photonic fleet are disabled.
A player can only select 5 consoles that are active. This means whether you have a 9 or 10 console ship, its fair. Players can still use their consoles they paid for as 5 consoles slots should still be ample to use several paid consoles.
Only 1 duty officer slot will affect their set up.
This set up will be switched on when ever someone enters a PvP match and their PvP set up automatically shows. when they leave it goes back to their PvE set up.
Fleet ships and lock box ships are docked their 10% extra bonuses to hull, shields etc.
The new PvP reputation system would be a big factor in providing bonuses in PvP only. This means if players want to unlock new abilities and get an edge the way to do it is to PvP. Any player can obtain the same level by playing the game. No need to spend extra money on buying power. This would be the only aspect that gives some people an edge, but that edge is obtain by hard work.
This hopefully solves a few issue;
1) The huge number of abilities is reduced, meaning pvp comes more down to skill than who can chain off the right number of abilities. This makes it more like tier 3 PvP where its a little more manageable for new players and less hectic all round. Teamwork and tactics are the order of the day.
2) It will be less confusing as there are less abilities to pick from and be hit with making counters easier to use. It should also make it more balanced as everyone gets the same boff station configs (3 ensign, 1 lt), and you will know what a ship is capable of.
3) People wont have access to the mega abilities that result in almost instant kills giving people time to enjoy the fight rather than being blown to hell inside 2 seconds.
4) Higher up powers can be tweaked for PvE as much as they like as they will never be used in PvP again.
5) Much more restrictive set up will give PvP players a new challenge to learn as they set up their ships.
6) It should make it much fairer all round. PvP Should largely be about skill, and gear. Not cash spent. Leave that for PvE only.
7) The PvP Reputation system does not affect normal PvE, and thus attracting leechers, but does give proper PvP players something to aim for, and still provides the hardcore elite PvP players with that sense of superiority.