I agree. Large, non-pirate ships are just what we need. A Galleon is a nice idea - maybe using the "Jack Stone" hull and beakhead. That hull was quite galleon-like, and that's what I used mine for.
The Imperial Flagship is actually a Naval Cutter
. Lego has done a very nice job with it too. As a small ship this was a good choice, although I'm still waiting for some large warships!
I agree - the ship from the Imperial Trading Post looks awesome. (I wouldn't know, as I don't own the set - yet)
Considering Lego likes to have two factions in each set for instant action right out of the box, a set of two (one with the small pirate sail from Raft Raiders) would be even better. Pirates vs hapless merchant ship - Arrr!