First off, I don't think they're coming so let's get that out of the way... But honestly, do people actually think they're going to work? I don't. And here's why:
1.) It's not much different than server links -- Servers already get partially restructured every 2 months with server links. Guilds across servers already get put into a de-facto alliance, it's just not called an alliance. If anything, the 'alliance' system is just a more souped up version of server links. The population imbalance will still persist. If anything, it will be worse.
2.)Players and guilds won't change -- Try-hard players and guilds will still find a way to bandwagon and game the system. Instead of server stacking, it will be alliance stacking instead. You can have the best matchmaking system in the world for world restructuring that takes different metrics and statistics in mind, but it doesn't mean jack if players just stack the winning alliances and losing or struggling alliances don't show up due to attrition, demoralization, etc. This situation makes things harder for smaller guilds and alliances that are trying to resist them.
3.) Guilds will have too much power -- Alliances will eventually consolidate into powerhouses limited only by the yet to be proposed alliance cap, dominating smaller ones either through victories, bandwagons, or both. So, as with the current server stacking and through historical bandwagons over the years, attrition eventually sets in as smaller guilds desperately try to resist the stacked alliances and people leave or quit WvW entirely out of frustration. Again, it's no different than the current situation. It will be Blackgate all over again but with guild alliances. Due to people quitting, the matching system will get to the point where it cannot find an opposing alliance of equivalent strength, so the system breaks down.
Thoughts to this?