How would you combat the droves of ninjas and guild destroyers hopping from guild to guild?

#2 - so all progresion oriented guilds can now demand you skip server after the raid Wed night, thur night, fri night, sat night etc so you get 7 full raids in per week to max out progression. Hmmmm think this is wrong.
Next problem - is one you dont think of in the US as much - what about language? In mumble do you speak polygot so everyone understands? Stick to one language? So the number of servers is divided by the languages as some are language specific. Even in america I am sure there are different languages (French canadians, Mexians, foreign nationals, heck even the 'gang speak')

#3 - teams only...so flexibilty is out the window eh? So what if fred the tank cant make it tonight - ok we cant raid then as we only have him in the team? What about the rest of the guild? This is too specialisted, and too exclusive.(As well as Elitist).

And lastly (perversly) #1
I actually agree - the guild should NOT be as important with the perks. But I believe the guild XP thing is a mistake, as it could lead to people hawking their 'XP' on the open market, or trying to blackmail their guild etc etc.
I think guild rep should be handled differently as well, guild rep should suffer loss when you leave a guild, but it should be easier to grind back up with a new guild. Something like 10-20% loss when you leave guild, with each time you leave guild within a month adding to the loss of rep (quickly) like 15% first time, 30% second time, 60% third time, 100% all subsequent times. This will help with the guild skippers, while not significantly impacting the people who have to change guild for various reasons (moving server due to RL, guild disbanding, etc etc).

#4 When PVP gear is no longer allowed in PVE situations, THEN and ONLY THEN would I even think about possibly agreeing with you. Your PVP gear spoils my PVE - but its ok then, but now the PVE gear spoils PVP - its a problem?

@Sinthar:

#2 would obviously need the exploit where raid locks reset on realm transfer fixed.
Also, I believe WoW's backend to be a gruesome mess that has been festering for 7 years - either that, or else Blizzard is flat out lying when they say they must charge for character transfers due to the work involved. If WoW's backend is as bad as I think, Blizzard would have to overhaul it, perhaps from scratch, before some features - such as free transfers - could be implemented, and this overhaul would hopefully fix the kinds of bugs and exploits that can be triggered nowadays on realm change.
BTW: with a properly done character database enabling free, instant, and unlimited realm transfers is quite feasible. In fact, a number of MMOs, managed by quite smaller companies than Blizzard, are able to offer free and unlimited transfers at the click of a button.

Free transfers would also help with the language barrier. When players are free to apply for any same faction guild in the whole game, the chance of them being able to find a whole guild that speaks their language is actually much higher. BTW, I know the problem first hand; I'm from one of those South American countries that don't speak English and where WoW's subscription is roughly $8 :)

#3: My intent is for smaller organizational structures to be possible and supported, and for them to be able to exist outside a guild if the players prefer. I perhaps didn't express myself clearly, in that I don't actually want the same restrictions of Arena teams regarding who can enter the instance.

#1: If the guild is large enough that it can remain at max level even when a couple (or perhaps even a couple hundred) players leave, there would be no way for the player to leverage his share of Guild XP as blackmail material. Also, if the player is actually willing to blackmail his guild, perhaps getting rid of him right away is the best course.
I also don't see why guild skippers are any problem. In part because I believe making players stay in a guild just to not lose perks or to avoid a new rep grind is actually worse than any problem guild skippers might bring.
Players hawking their Guild XP on the open market shouldn't be any more problem than players with high end raiding gear hawking their skill (or, more precisely, GearScore) for prospective raids. They would serve as a jumpstart in the guild leveling process, at most - and, arguably, a way to jumpstart the guild level might be a good thing, given the recruiting problems new guilds currently face.

#4: If I get a PvP-clad player in my LFD runs, the group gets to choose: either I leave or the PvP-clad player does. BTW, I only play Tanks and Healers, so either way, if I leave, the group should be looking at a reasonable delay while the LFD finds someone to put in my place.
I believe this answers how I feel about players using PvP gear for PvE.