1) Implement a system where a player will not receive faction for losing if they AFK in their base (kind of like how a player will not receive experience if they don't participate in a fight in some manner).
2) Give rewards/bonuses to individual players at the end of the fights based on their performance. IE, top kill counts, top ress point cappers, top healers, etc., will get faction point bonuses. This will greatly discourage AFKing, in my opinion, if a player can still get a nice amount of faction even if their side loses. It would also promote more participation in general, since this will appeal to people with the mindset of "my team will just lose anyways and it'll be a waste of time."
3) Display these rewards in a summary screen at the end of a match; that way players can see a breakdown of what happened in the match, kinda like the way Battlefield displays statistics at the end of a round. Doing this will give quantifiable evidence that a player's skill does matter, since everyone who participated will notice, "oh man, that Bob guy's good. Even though his team lost, he still got a bunch of faction." Or, "man, Bob's good, he got 1,000+ from winning AND having the top cap count." It'll also encourage continued play if a player can see how well they are doing with numerical proof.
I always wondered why #3 was never a part of the game in the first place. PvP in GW is akin to a strategic 3rd person FPS, and in every FPS game I've played online, there has been some sort of summary screen at the end of a match. I don't think this would be very hard to implement at all.
I was tempted to put "punish players for leaving early" but I don't think that will work for a variety of reasons, and will end up causing more trouble than it fixes. I think giving players more incentive to participate and do well will cause less griefing...hopefully

On another note:
-Add in a larger version of the minimap for the 12v12 arenas, like the map you see when you hit U, but one you can ping and draw on. It's kind of useless to have people pinging important locations when the shrine/fight is out of the display range for your minimap.
-Let me know what you think
Thanks for reading,
Wayne =)