If they have server transfers right off the bat it might not be too hard to keep a guild going, but otherwise it's gonna be as much of a pain as it was in vanilla. Yes it's hard to find 40people who want to be competitive. It's especially hard if you're not currently the first guild on your server. I mean obviously in a perfect world you're the #1 raiding guild in the world and you get applications like justin bieber gets lovemail, but if you're not but still want to do cutting edge raiding, it's hard as all fuck. The best guild will eat all your potential recruits, will eat into your current members who are tired of having to deal with the retards and not being able to progress because of a lack of good applications, and eventually either die out or turn into a casual guild.
It was horrible then and it'll probably be horrible again, I just don't see any good way to get around the problem of recruitement, attrition and so on which are amplified a fuckton when doing 40man raiding. Oh and all the people sitting out, since you'll probably want a 60ish ppl roster at least to run 40man, so you'll have to do scheduling and shit.
Running a competitive raiding guild in vanilla wow was a fucking nightmare.
As for warplots, they've said they'll drop best loot? It seems a bit weird they'd make those drop best loot instead of arena. While I never liked arenas too much in wow, it made perfect sense to me that the best loot was from them, because it's the mode that required the most dedication/skill(well until people figured they only had to play a bunch the first week of a season then play their minimum matches every week until the end to maintain ranking).
Running old AV in a guild vs guild(until they fucked up the sync queues) was definitely fun but wasn't near the amount of skill required, mostly it was general strategy and whoever had the most good aoes to break the chokes, mostly mages spamming blizzard and AP/PoM/Pyro to take out a healer out of position, rogues trying to not get hit by the waves of aoe to assassinate healers and windfury warriors once the shit started crumbling to slaughter everyone left.