Right...Removing factions and replacing it with a Capture the Flag mini game is exactly what everyone wants! I forgot. All it needs is a boss monster at the end of every cycle, and it'll be complete.
Capture the Flag is a lot of fun, they just need to do it the right way. Making an arbitrary battle over a shrine isn't the right way to do it, IMO, but it can be done, and it can be fun.
The main problem is creating a system that makes it fun on a sliding scale so that all shards can benefit. Unfortunately, whether you're willing to like it or not, that's going to have to require some AI mobs on smaller shards. I just see no way to create compelling PvP situations on shards like Origin, or Oceania, without some kind of AI incentive.
I've heard way too many PvP types balk at the need of PvM to initiate PvP. The PvM doesn't have to be the main focus, of course not, but there's a reason why MOBAs are so popular. Simple PvM can add another element to a PvP battle which makes the "war" aspect more tangible, and gives the strategist something more to think about.