The boat controls quite smoothly. I'm curious if the running shoes will end up having an effect on it, though, because of how it's likely done (as a player sprite replacement, I assume) (obviously couldn't test this, because couldn't get back into the PC's house to get them).
The fade-out-fade-in used when the young man picks you up is similar to what I was suggesting, rather than the protracted travel of the old sailor. However, the screen dims noticeably after boarding the boat that way; it returns to normal brightness once you dock. (Actually, I think it dims when you enter the old man's boat from the western rayquaza and gym docks as well.)
Getting on the old man's boat on the western dock on rayquaza island is a bit borked - the boat stops too far away and so the PC walks over a tile or two of water.
If you dock at gym island, then get back on the boat and dock at rayquaza island, and then travel back towards gym island, there is a copy of the boat docked there already (you can't interact with it, and it disappears after docking there).
Which dock tiles can be used to exit the boat are different for each dock. Maybe use an indicator tile. (I almost thought that the eastern rayquaza dock was broken, until I checked the left side. The first two docks made me think that the broken-dock tile always indicated an exit.)
You might want to make the old captain's accent a little thicker - otherwise, 'me' might be misconstrued as a typo of 'my' rather than dialect of 'my.' (That is, right now his first few words are too normal-sounding. Even simply throwing in a 'Yarr, [boyo/lassie]' before he says anything else would make it immediately obvious how the player should be reading his dialogue.)
I heartily approve of "Get on, ye kid!"
Instead of "Hmm... I need to find a way there." maybe use a less generic "Hmm... I need to reach another island." Using the pokenav call function is cool, though.
('How did you get here?' lady's text is slightly borked ("ç Áow did") - easy to miss.)
(Trying to talk to the guy in front of the Rayquaza statue froze the game, btw. I assume that's just because of a incomplete script, but it could be something overlooked, so I bring it up.)
(Rollout move tutor is out-of-place here, btw. He's on a tiny island! Where is there to roll!)
The Rubies standing on water in the upper left is hilarious btw. (I knew I shouldn't have let the PC take a swig of that old seadog's ale!) Now I want to hear a sailor/fisherman on shore leave talk about the cabin-fever-induced hallucinations he experienced while travelling/trawling in the waters north of those islands ;)