So navigating the horde ship and the great seal is a bit messy.
I came up with some ideas how we could make it a little more practical. Feel free to give some feedback.

Firstly, there are 2 mission tables on the ship with a kul tiran map on it: in front of Garona, that's the one you can actually use to launch missions, and in front of Nathanos, that's the one that you can't use for anything (maybe a quest or two?).
My first suggestion would be to delete the one before Garona and use the one at Nathanos as our main mission table. This way it looks less dumb cuz now you only actually have one mission table.
Secondly, move both Garona and Eitrigg to stand around the new mission table with Nathanos. This would just make it easier to access both troops, upgrades and mission from the same clicking area. This is already the case to some degree at the Alliance ship with Shaw-Alleria-Mission table.
This is how it could look:

Next, I wanna tackle the awful travel route between the ship and the Great Seal. It's not too long, but it's just too many minor movement/clicks.
BUT there is already a solution for this that I have no idea why Blizz hasn't thought of: Lasan & Aviash.

They are already on the ship and could easily be used for one-click travel. We just have to move them a little. Also move Cromush to where Lasan was standing originally, Cromush does nothing anyways. Here is my suggestion in action:

They are already on the ship next to the captain doing nothing. Unfortunately that spot would be very bad for a flight point as they are directly next to a huge wooden ship part that blocks larger mounts and vision. BUT, we can move them where garona used to stand (cuz we moved her up) and that small open place is optimal for a landing camera angle thats looking at the entrance to the ship.

Additionally we can have Aviash be at the Great Seal on that little column next to the flight master. This way if you click Aviash on either side it will just fly you to your ship/the great seal instantly like a Pa'ku totem. No extra menu pop-up, no 'click okay', you just click it once and you already fly.

My last suggestion would be to move the unlockable mission table at the Great Seal to the little training area (as it fits more thematically) and also add Usha Eyegouge next to it, who you could use to recruit troops (same way as Garona at the ship). Right now the Great Seal mission table is basically useless because when your troops expire you just don't wanna send followers on new missions without recruiting more troops. But you can only recruit troops on the ship. So it's just pointless. This way players can actually choose where to do their missions. Here is the idea:

So, that's it basically.