Ghostcrawler and other Blizzard staff have talked about the removal of the Guild talent tree lately, and since then have been bombarded by requests to put it back in. Here is an excellent explanation from Ghostcrawler on some of the potential issues they saw with it.
Looking over his explanation of issues I can really see it happening. If I joined a guild to raid, but the guild leader decided he wanted to focus on PvP or PvE gold/leveling talents, I wouldn't be happy. Also depending on what the raid progression talents focused on some DPS might feel they would be better in a different guild.
Even if you were a raider, and the guild focused on raiding, I can see issues that could pop up. If you and several friends in the guild also focused heavily on Arena combat each week, what would you do to compete? Would you be forced to setup an alternate guild and level it as well, switching guild membership to compete in your arena fights, and then switch back for your raids. If it didn't apply for arenas, would it for battlegrounds? Would you get wiped if you were not in a PvP focused guild and then guild hopping would apply for that?
While I really like the idea of each guild being able to be different and unique, I can see now that it could indeed cause issues. It's nice to know that Blizzard is looking after finding issues before they effect us in the game. I would still like some way to make guilds unique though besides just the tabard system, which most people do not display anyway.
To read the latest guides, news, and features you can visit our World of Warcraft Game Page.