Instead of automatically placing everyone on the map after they choose a server to merge to, can everyone start with their towns off to the side (or in their inventory), until they place them themselves?
I know we get the free town moves, one per town, but the problem with placing players on the map automatically creates a "traffic jam" for lack of a better term. Meaning you might want to move your towns somewhere, but someone is already there, and you don't know if they plan to move or if they've already moved to that location. And they might be waiting for someone else to move, or looking for a new spot themselves, and so on. The board becomes more and more cluttered as time passes. It's worse when you're trying to coordinate with 20 other people in your alliance.
Maybe you even moved half your towns and someone suddenly spawns in or moves to the spots you were going to take, and now you're kind of stuck having used half your free town moves.
I just think starting with an empty map will make things more clear, less of a "traffic jam", less clutter. If you see towns on the map, then you'll know that person has for sure chosen that spot, and you don't have to wait for them to move.
It's still a first come first serve system, just without the cluttered map.
As an alternative, you could give everyone unlimited town moves for the first week so everyone can work through the traffic jam. That way if you move some of your towns and realize you need to move somewhere else, you don't have that feeling of dread xD. Or you can temporarily move to let someone have the island you're on, while you wait for your own spot to open, without using up free moves.
This is especially needed on server #2. I speak from experience. With 7200 players, that "traffic jam" was a nightmare, even if you're one of the first to sign in. I even considered quitting with this merge because I didn't want to go through all that again.

