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Add 3 guild halls, and give them to the top 3 guilds, put them somewhere in the main city, close to each other. Make it so that only the guild leader can invite/kick players. Make them huge and really pretty.

Nice idea.
But there will be a slight problem, how do you decide who the 3 top guilds are?
Frags? People will simply kill noob characters to boost them.
Vote? Don't know if that would turn out that well, also doesn't really matter how good you are, it's more like how famous you are.
Decided by the rebirth of the players in it? As we all know rebirths aren't everything.

add event "WAR OF EMPERIUM" too

Well the idea its nice, but as gollum pointed, we could have some issues to decide which guilds would get the castles, one good idea would be the 3 guilds with most total reb (the total of all member's rebs) and I'm not "ok" with the "invite players" thing, we have or own houses for that, the guild hall should be only and exclusive for the guild members, would be nice also if inside the members could have some little advantage, like one private small spawn of some monster, and fastest access to some areas, since vip isnt very easy to get now (only with vip medal / buying from others mini vip) the !fly system isnt very usuable now.

Seem very cool :P

Maybe the guilds with the most total guild war wins? If admin has some data on that from previous wars, use that and if not then starting from the last guild war? It doesn't have to be 3 guilds, could be just 1 guild.

I thought about that too, but it doesn't necessarily mean that you are the best guild if you win the event.
Might just have been lucky enough to take last hit. (Sorcerers new spell ftw!)
So in the end it's a really hard to decide the best guilds.
Yours sincerely,
Gollum

Well since theres usually a 50/50 chance to get the nexus (depends how many decent guilds actually participate) I think it would be the best estimate for the best guild.

Maybe the winner would still be the one who takes last hit.
But they could track the data what guild made the most damage, which then is rewarded with the guild hall.
Yours sincerely,
Gollum

Guild Bob is first to get into the event, they start blocking the bridges, gets set up and everything. Guild Fred enters the event, they try to break through the defenses but fail for 5 mins, the nexus is now at 49% health, Guild Fred finally manages to get through kill everyone in there and kill the nexus, and Guild Fred it down from 49% to 0 and wins the guild war, no guild hall is awarded to Guild Fred since they didn't do the most damage. I don't think thats really fair. Anyway it should be for the last hit, if the guild is a lot better and deserves the guild hall, then they should be able to block the other guild out.