I am happy to see more games adding these kinds of features.

Ragnarok Online has a similar guild system. Guilds level up from player experience (although it does actually take from your leveling exp) and the guild must hit a certain level before you can take a hold a fort. (like WAR, anyone can fight but you must be an established guild to take/hold)
Also leveling up gives you abilities like players getting buffs from being near the guild leader and the most important ability comes in the form of the leader being able to call the guild to himself.
Although in RO the flags are only used to teleport yourself around the fort. (to give a defending advantage)

However I REALLY REALLY hope that they put some kind of size cap on guilds in WAR. With a size cap it becomes more about player skill, guild strategy and forming alliances rather than just who has the larger army of nublets to zerg rush in.

RO has a size cap and although there arn't enough players left on the game for most guilds to even hit the cap, in the past I think it really helped to keep the PvP wars more about skill and less about sheer numbers.

Lately I had been feeling disappointed by a lot of the news coming out of WAR but things like guild wars are what really matter and what can make the game fun.
I've always thought guild VS guild is where it's at, who actually cares about their 'faction'? Most people have characters on both sides in faction based PvP games anyway. However guild competition is very fierce. It is much more fun to fight for the honor and glory of a guild that you really feel a part of rather than a faction of faceless people driven by NPC story.
Don't get me wrong, I love story lines but they arn't as effective in driving pvp.