I have been RA 5 for awhile now, and PvPed most of the way up. Mind you, I haven't PvP much before in games that have PvE content, so this is moderately new for me. I also have read the up coming changes for PvP, and while welcomed, won't fix the issue.
1. OP abilities. Yes, I am gonna rant about Viral Matrix and whatever that other one is that forces all of your cooldowns to be long. They are OP.

When I use them and when used on me. Yes, Science Team can remove it, but come on, one ability only? I am an Engin and Use Engin Team III for my hull. I pop that, and boom, I'm hit with VM. I get the point of it, but, have it kill random abilities, not my entire ship. It's the I WIN button still for whoever uses it unless that player ensures that he always has a CD available for the Science Team.
2. Queue's - They suck. My last match before this post had like 40 feds waiting to get into a Large Salvage match. So, you think I would go in, find a bunch of feds and no klinks. Nope. Instead, Feds had lost about 300 or so points, the map was full of klinks, and I was the only fed. Now, it could have been a pre-built team, but, I strongly doubt it. Matches shouldn't start till both sides are full. Champions Online had this, why not STO?
3. Cloak - It's not OP! But, if matches can't start until all sides have 5, 10, etc. then either require the cloak to drain power after a set amount of time (like going reverse) or give Fed's cloak. It's not OP, I kill klinks who zoom in and out of cloak. But, when there is one fed, they have to get ganked over and over while waiting. One klink, they can sit far back and wait for the most part.
Honestly, a lot would be fixed if the queue system is fixed. Fed vs Fed matches will help, but, the same issue will arise there. I enjoy PvP when the matches start out fair. When it doesn't, it sucks, it's not fun, and I let myself get blown up over and over till it's quickly over.
Oh, ground PvP is top notch, except the queue thing.
Comments
1)OP abilities- just deal with them. Yeah there is SNB, it can be used every 75 seconds. For VM you can have Attack pattern omega running and it will not affect you.
2)Ques, talk to Cryptic about why there is no Klingon content. No Klingons= very long ques for Federation.
3) If you are all by yourself, don't respawn until more team mates show up.
not everyone has APO and even if you did you could not use it or anything else when someone hit you with a 30 second SNB usually followed up with vm
I'll agree with you on this.
The number one thing I would like to see changed is different types of PvP,
also open PvP
PvP isn't that much fun when you are pugging though as 90% of Feds suck big time.. I still get people who know nothing about FBP and SNB and VM..
Queues suck right now, but FvF is coming this thursday so it's gonna be OK after that.
viral matrix is ok as it's counterable right now but SNB is overpowered and they're gonna introduce a counter to it soon so they're gonna fix it.
Cloak was never a problem for me.. for some reason feds cried over it a lot here in the forums. So they now introduced the cloak debuff to tactical officers (fire on my mark).. So it shouldn't be a problem for the people who know how to use it.
P.S. My toon is orion.