I seriously think the only way around this is to create an all new Guild Warfare and Arena, Apart from the Realm GW and Arena's we already have. Each Realm should have it's own cities like now, plus the server should have 10 main cities that the entire server can compete to capture, once they reach a certain guild level. By this time, we can assume that the strongest guild in each realm will have most of the good realm cities, so in order to not create super guilds, we put a cap on the Sever GW cities. Maybe 2 per guild. This way there is constant fighting going on to gain the buffs from the cities you don't have. Just as long as each city has a decent buff, you can bet that GW will liven up quite a bit. As far as the Arena is concerned, a server wide Arena would be great for the higher level players, giving the lower level players more flexing room in the realm Arena's.
I think we have come to the conclusion that this is the only answer to the issue at hand.
Please excuse the bad grammar and capitalization, it's 2:42 am here and I'm whipped 