BOATS. Yes, I refuse to cease wishing for boats. So here is what I've been thinking in terms of boats. This is of course an idea that will likely never come to fruition since it would take a lot of coding. But, given the popularity of fishing, boats do seem like a logical secondary 'minigame' of sorts. Also boats would just be fun!
With Aetolia's current design, there is no need for boats so far as travel goes. Boats could instead be a buy-in skill that is part of a faction group, like fishing, that then rewards the player in terms of quests + some small exploration opportunities tied in with them. These quests and exploration opportunities (little islands, often containing the quests) could result in gold, tradeskill ingredients, or other small items (such as collectibles). More skill ranks (gained through doing boat quests) leads to bigger and better boats that can get more quests and go more places.
Fishing could of course be tied into boats as well, with boats allowing access to new and interesting fishing areas. Have fishing but can't afford the boats skill and want to go to a boat-accessible fishing area? It would be a great opportunity to make some friends with boats, since what good is a boat if you can't have multiple people on it (with the number of people allowed scaling up according to the size of your boat).
When you first buy the Boating skill, you would get a nice little two-man rowboat, not good for much apart from some minor errands for the Dockmasters. These errands would raise your faction with the Dockmasters, and as your skill goes up, unlock the ability to purchase progressively bigger boats. At transcendent Boating, you gain a large boat with a good-sized deck, a couple cabins, and a hold, with the ability to customize these at a (expensive) cost. All boats could of course be named for a small fee (like a minipet).
The special fishing areas would just be a nice addition to Boating as well as Fishing. The meat of Boating would be in the boat-accessible weekly (or monthly) miniquests to be performed on small islands reachable by boat. The gold offered from these quests wouldn't be immense, more like fishing gold, but special tradeskill items could be found, whether dropped by island mobs, spawned in certain locations (island fruit, as an example), or perhaps dredged up in the harbors. Small items like these could also be a common quest reward, with some sort of collectible line offered as rare rewards (a collect-them-all sort of thing, like the figurines that are now in the ranking system).
So, yeah. Boats. Boats would be awesome.
TL;DR- Make Boating a skill like fishing and part of the faction system. Make them for minigame-type quests instead of travel, since we don't need them for getting around Aetolia. Go fishing on a boat! Sail the Beryl Sea to get gold and new tradeskill items and other shiny things. Customize boats for a goldsink.