I talked to Matt about some of this via IRC, but here's some of my thoughts organized here for the forum readers.
1. We're going to have (the guild has been built, just need to finish the fighting so everyone has time to join) an empire-wide guild. Now, Arcaea currently has discussions in three main ways: The whole realm, the Phoenix Court (where most everything gets discussed), and the Military Conclave. The guild is going to simulate that with the all guild, full members, and elder members. The idea being that a good portion of the conversations will shift to empire-wide instead of realm-wide, helping with the unity problem.
Depending on how large your guild gets, with the people of three realms in it, I think you're biggest issue will be message traffic. I stepped down as leader of Sanguis Astroism on Dwilight so I could get away from all the messages. I just couldn't handle the flood of traffic, hundreds of messages in a couple hours, when some topic came up that *everyone* had to argue over.
And in guilds, you can't have separate channels like you can via the realm message groups. Everyone in a tier automatically gets all messages to their tier and all the lower tiers. This means that Elders can't escape the rabble.
2. I fully anticipate that over time (though probably a long time for Jenred if he stays in the position) people in one of the other realms will decide they don't like someone from a different realm being in control. This is one of the (many) reasons why there is going to be an internal war system with internal rankings. Each realm will have a rank, which will also determine what percentage of their taxes have to go to the Imperial throne, and the highest ranked realm chooses the Emperor. The Emperor then stays in position until their realm loses their rank and a new Emperor is chosen. Ranks change via a formal challenge where no outside assistance is allowed and the two realms fight from the first day of Spring to the last day of Autumn, with the winner taking the higher of the two ranks and the loser the lower of the two ranks in dispute. Determining winners and losers may be non-trivial in some cases, but I think a system where the loser is whoever has the worst change in weighted production (production of a region multiplied by its population) on a percentage basis over the course of the challenge would work well enough.
Ritualized combat? What if one of the realms is in danger of wiping out the other? How far will the Empire let things go before he steps in and stops it? War without risking your life, or the life of your realm, is a bit stale.
5. The empire is certainly going to have the one position per family per realm rule Arcaea does now (at least after the initial colonization stages where it may be unavoidable) and I'd really like to make it one position per family for the entire empire. The idea is to suck as many interested people in as we can by making positions more available than they are most places.
I hope you get enough people interested in that many positions. That's always been one of the most difficult things I've encountered lately: Finding enough volunteers to fill position vacancies.
I'm sure I had more ideas/comments, but I don't have time now to write them down.
