Celebrim
Legend
I think that is the strength of 4e's skill system is that while you certainly won't be trained in everything you ARE likely to have pretty competent bonuses at least 1/3 of all the skills in the book
Only because the skills in the book collectively cover only a small percentage of things one could be good at, and only because the overall approach of 4e retains 3e's overall passive approach to skills (compare how skills are used to how class features are used) - but let's not turn this into an edition debate.
While the number of skills in my game is larger than even RAW 3e, the ability of a group to span competency in a large number of skills is no less. An 18 INT human rogue would be at minimum 'proficient' in 16 skills. I have six players in the group, and there are two skill monkeys in the group, and a multi-class character that has dipped into skill monkey. Aside from captaining a large sailing vessel, the party has pretty broad competency. I'm not terribly worried about whether for a given scene someone will have an obviously relevant skill, much less a very specific 4e problem like can you use a spell or class ability in place of a skill check to gain a success if you are playing RAW?
What I'm worried about is creating a range of scenes where everyone's different skills (whether literally skills or class abilities or spells) will be potentially useful, and equally where the color of the scene and its resolution are diverse. Of course in such scenes I could default to ability checks, but ability checks are generally unreliable. The important point is that if you are skilled in my game, you can reliably propose actions on the basis of that (because unlike 4e, difficulty is not expected to scale with level) in the exact same way you can reliably propose actions by casting a spell (in 3e) or by using a class ability (in 4e).
As far as the broad conflict here, they are racing to catch up to the BBEG who is an another ship (one better suited to this voyage). How well they handle the voyage determines how far behind they are, and as such, how time crunched they are as well as (for some complicated reasons I won't go into) how they'll interact with the BBEG and what the BBEG's plans will be. There is also a specific conflict between the PC and a deity playing out here which is directly tied to character background. This scene is intended to bring that conflict to the player's attention in a very climatic way, and is likewise intended to be the climax of the voyage (all scenes after this event are intended to be either denouement or side quests). Ideally, if all goes well, the outcome of this scene is 'You reach the island with few further incidents'. (Though of course, I have plans for all eventualities).
Some of the suggestions above like mutiny, sea monster, and sahaugin are planned events that feed into part of the journey's central structure - that is, the ship and crew are the real 'hit points' in the journey. The ship has 105 crew. It requires a minimum of 25 crew to properly run the ship (and that with some stress). Likewise, the ship has a set number of hit points. The structure I'm planning for this journey is less, "Protect your character" than it is, "Can you protect the ship and crew." So I already have something like a 'skill challenge' planned and designed with several sea monsters, where how fast and efficiently they can dispatch the threat largely determines not whether they get injured, but how much crew they lose. If they get to the hurricane with a beat up ship and crew that's largely been eaten by monsters, and don't resolve some problems in ship's morale and so forth, then the hurricane is going to be an almost insurmountable challenge and the ship is probably going down. If on the other hand, they do resolve those problems and take care of the ship then I want the challenge to be scary but not particularly threatening - NPCs can handle the ship, and the PC's assist in various small ways to protect the crew. I do however have 2 skill monkey's that can directly help with skills generally superior to the NPC's on the boat in every regard but actually sailing it, so I want to get them involved tying down rigging, reefing sails, cutting lose torn sails, and so forth. The rest of the PC's have no business being above decks during the height of the storm, so I'm particularly interested in ways to keep them involved so that they aren't merely passengers in the scene - manning pumps, closing hatches that are ripped off, helping the carpenter patch leaks, tying down cargo that breaks lose, treating injuries, and so forth.
Right now my biggest worry is pacing, because I have no plan for putting this all together. My ultimate goal is to have a set of 'timelines' with parallel events in the hold and on deck that together tell a dramatic and exciting story, which is going to climax in a 'rogue wave' that is anything but a rogue (it's actually a very obedient wave).