This is just my observations, but I'd like to see other people add in what they think should be added to improve the PVP experience.
I'm not calling for nerfs or anything like that, or changes to either side, what I'd like to do is identify functional changes that could improve PVP in general.
Auto Team OR the ability to see allies on the map.
Right now you can only see team mates or allies if they are close by. When you zone into the instance you should be able to instantly find out where your allies are on the map so you aren't left searching.
Limit PVP launches until the teams are at least 2/3 full on each side and provide a staging area before the match starts.
As it is, most Klingons are queing up constantly for PVP so they start with a full force of 5 players, while Feds just trickle in as they remember to queue. The result isn't pretty and we've all been there. A solution to this would be a 15 or 20 second wait before ships can move when a match starts to allow the teams to zone in and get ready to fight as a team.
I'm sure there are more things people can think of, lets see what we can come up with. Please try to be constructive.