Outside of not getting credit for PvP wins (fed or klingon side)... I really don't care for PvP (aside of no bonus for participation) and am just doing PvE repetatively (klingon needs more PvE missions). Can you tag PvP missions somehow so i don't waste time taking them and dropping them?
Going on the no bonus for PvP comment, why PvP? What do you gain from it? Some <blank> items from a vendor? PvP has no effect on the game, therefore is pointless with no draw for the common player. Not that it's just cryptic. A lot of games PvP suffers this downfall. Guild wars doesn't have the best PvP set up (except fort aspenwood) but for their big faction wars in Factions, whomever was winning the faction war would make it harder for the other sides PvE. Maybe have a station with special vendors or something that can shift hands in the neutral zone that offers special items/unlock/missions only at that station when your side controls it. Or NPC spawns could increase/decrease level depending on who is winning PvP.