Edit: If you don't feel like reading the entire wall of text, just read the bolded, underlined, and italicized statement.
I'm a fed in T3 atm and I pvp quite often, always with pugs, because I have yet to find an active fed pvp fleet. Today, I was playing on the king of the hill salvage wreck map, pugging with some fellow feds. We were playing against a group of klingons that executed attacks with pinpoint precision and were rolling us completely. They all had similar names and were extremely well organized, probably because they used voice comms, so it was safe to assume that they were a premade group.
This is an old story, not unique to STO in any way: Premades owning pugs. And there's nothing wrong with that. Good organization, good communication, and good teamwork that come with a good premade should, 99.9% of the time, be able to triumph over a pug that never played together and has, at best, average communication.
But the problem in the situation was simple. The Klingons were completely rolling us and there was little we could do except slow them down a bit. But why bother? Things would only go faster if we simply sat at our spawn, protected by turrets,and let the klinks hold all the points (they were doing so anyway). We couldn't get too many kills because they had excellent mutual support and heals; they were an excellent group. So I explained this to my team, they agreed, and we spent the last three minutes of the game waiting for our xp.
With a minute left in the game the klinks asked us why we stopped fighting, to which we replied that there was no point, we weren't getting kills or holding points, we were just dying. A premade, especially an exceptionally well organized one such as there's, would always roll PUGs like ours. We might as well get it over with as quickly as possible, get our xp, and be on our way because exploding repeatedly without making the enemy explode is simply no fun.
As i said earlier, this phenomenon is not unique to STO, but is endemic to nearly all games where pvp is an option. However there is a simple and elegant solution. Have two sets of PvP queues, one for general pvp where pugs and premades can go at it, and another where only individuals, not groups, can join, a "random team" option if you will. This solution has worked in many games in the past. DotA for ******** 3 had the shuffle players command, Modern Warfare 2 had the "Team Deathmatch" (Pugs and Premades) and "Mercenary Teamdeathmatch" modes which operate exactly as my "general" and "random" pvp queue suggestion.
In every game where this was implemented, it had a positive effect on the game as a whole. Premades fought premades more often providing for more interesting and challenging games that were more fun for all involved. Many pug players still stayed in the regular mode, adding a bit of variety for the premades and the pugs. And, more importantly, PUG players that wanted nothing to do with premades or simply couldn't play with their friends/clan/fleet at the time for whatever reason were able to play with and against other pugs.
IMO, it is a win-win solution for everyone involved. Also, I humbly submit that the pug only or "random" option will directly lead to fewer "NURF X", "BUFF Y", or "Z IS OVERPOWERED" threads.