I think I am an expert in this subject because I have PvPed since Doom II the grand daddy of PVP, I was in on original Team Fortress, Quake 2 multiplayer mods, TFC, many Source Engine mods, and other games that were PvP based. I've seen PvP in other MMOs as well.
Make the game even! Nobody is going to stick around and get killed game after game because of one unbalanced factor or another.
*KDF and Fed should mix members so if one side is released a heavy advantage on a patch the other faction isn't screwed. I don't like people who are faction elitist making them co op with both sides will discourage the attitude.
*Team Scramble! People DON'T NEED to stack teams or form super premades in regular player vs player games, in fleet vs fleet premade is expected. But just to make an average group of players cope with a premade super team is pointless they have very little chance of winning. And on the other side of the coin that premade-team isn't being challenged so the difficulty for them isn't what it should be and they are exploiting the reward system to acquire loot faster then they should be. Another benefit is rather than having the premade team sit in a corner with their secrets they are encouraged to try and coach everyone and teach them what they know which is what a community of MMO players should be about.
*Shooter mode should be in first person, having a big hunk of your player's torso, head and arm in the way of the screen is confusing and blocks what ever is in front of me, additionally I've never seen a successful multiplayer shooter that didn't use the first person angle, Over the shoulder is more for single player games.
*Head-shots, body-shots, limb-shots or else what is the point of aiming? a good shooter has weak points and strong points, the head- the hardest point to hit usually does a satisfying amount of damage, I've seen crippling legs in TF and TFC and nobody really liked it, my favorite class was as a sniper so I was the one who did it and I didn't really shed a tear when they took it out for Team Fortress 2.
*4 teams. Yeah I know you don't see it very much in any of the games I have mentioned (Murderball in TFC had 4 teams) but I think its neglectful to ignore the possibilities of having 4 teams against each other, it makes a map fast and exciting.
*Modes: These PvP modes are open community as far as I know because I have seen them in a lot of different unrelated games.
King of the Hill: It's one point and teams compete for points to hold that area until the time limit is up.
Capture the flag: Classic paint ball style multiple teams each with a flag when one team gets the others' and brings it to a point they get points until the time limit expires.
Capture the point mode a: One team defends while the other team captures points up to their base and then captures a final point at their base to win, in some cases the next capture point is locked off and a respawn and timer is started so the defending team has time to build up defenses at the defense point.
Capture the point mode b: Both teams compete to capture the points up to the base and they can struggle back and forth over points so that they are both on offense and defense.
Hybrid Capture the point and flag: This is a lot like CtP mode B except instead of a final point they have a flag like in traditional CtF(Capture the flag)
Destroy the structure: These are a lot like Capture the point except instead of capturing something the players are destroying something, typically a building or something.
Real Time Strategy Gamer Mode; The Ultimate, probably best for last mode I know of is RTS mode, One player sits in a booth or something and relays orders to other players from an overhead view, they also place structures, vehicles, respawns etc. on the ground the teams compete to destroy one another or there can be other goals. I have seen Star Trek space RTS in Armada it was a good game Homeworld did an amazing space RTS too. Ground won't be hard to imagine either.
*Consider Max DPS since this is a RPG, No skill one shots are annoying, and people use them to be annoying, winning should be based on skill. Annoying people with no skills should be easy kills. If they are annoying and they have skills thats great it antagonizes people to play better.
*Don't make super gear that only a few people have access too. This just goes back to general balancing.
*Reduce NPC Spam: People don't need fleet support, spam turrets(needs a better timer or something), support officers, 36 fighters(Though carriers do need a good wing of fighters to support them), etc.
*All day maps, some people just want to plop down and PvP all day, they don't need maps to end and then wait several minutes for a new que to build, just make maps where people can join or leave whenever they want, get rewards for amount of time played and accomplishments but more for time played to discourage hopping. And Scramble teams when needed.
*Since Hypos, Shield charges, weapon charges, aux charges, engine etc consumables are a part of PvP, just give players either an infinite amount of those while in PvP, or else a limited amount with more available charges available at points on the map, but if you do that make it so each player gets an x amount recharge that can never be exceeded, and its an unlimited amount container, so everyone can loot it and no one can over loot it to get a hundred of something. Put those aid stations in helpful points in the map, you can even tie team ownership into a capture point so a captured point will only yield to that team.
*Seriously think about movement debuffs, it stinks being stuck and getting shot at.
*Walls need to be walls, with the exception of the TR-116a weapons don't need to be going through obstructions.