This sounds really interesting. Both options seem viable for different strategies and I'm honestly having a hard time deciding which is the better way to go (which is a good thing). The two 25-player guilds seem best for situations when two guilds are coming together and want to maintain their identities, and I can also see it being used for guilds with distinct parts (such as a pking/tower crew and a spar crew). That being said, a 25-player guild devoted to towering might have trouble against 50-player guilds which are entirely focused on that part of the game, but this will of course also depend on player skill, activity and guild focus on other activities.

Also, as Areo said earlier, I think it might be good to have an option in two-guild arrangements to chat only within your division, or with the entire guild as a whole. However, this could also be a bit of a problem because it would encourage division between the guilds, and I think it would be best if they work together as a cohesive whole.

Thinking on it again, I would personally prefer to be in a 50-player guild due to it being more unified. It would suck to have to worry about one guild not pulling its weight or something like that. Though I can definitely see situations where two 25-player guilds would be best.