Having read this and several other threads and various material from BtM, I think that treating ships in general as Constructs with the helmsman in direct control and other crew as riders seems like the best course. Given the results of the statistic analysis above, you could even give them hit dice! I agree that there's no need to give them actual ability scores except where they have a grappling or cone ram, and need a Strength for grappling purposes, and possibly living ships like those of the Elves and Thri-Kreen having a Constitution and FORT save. REF saves, by all means, based on the helmsman's, probably with a bonus or penalty based on MC. WILL saves are the helmsman again, possibly with a modifier based on the helm - I'm thinking along the lines of them being an enhancement to the helm, to help the user fend of 'jammer shock, illusions/enchantments aimed at messing with his piloting, and possibly disorientation caused by wake attacks from The Spelljammer with it's funky gravity plane, particularly warlike Dwarven Citadels, etc.
Note that this makes Bards the best class for helmsmen, since they're full casters, have good REF and WILL saves and will usually have a good DEX for the sake of their roguish skills. It's an incentive to have one in the group as more than "fifth or sixth PC" at least.
Making weaponeers take a feat to fire in mid-move is, perhaps, not quite as true to the original (as quoted previously) but in line with the need for Spring/Ride-By/Fly-By/Swim-By/etc. Attack, and can be justified in the ship often rolling on its axis as it moves to get better sail angles for full maneuverability, so it's only a stable firing platform (even if it feels it thanks to the gravity moving with the ship) in between maneuvers. As for the weapons themselves and their relatively small damage potential, I seem to recall looking in the 2e DMG and discovering that groundling siege weapons were wimpy then too. In other words, let the dirtkickers play with their little toys, in wildspace we use weapons fit for men!
I think that a method to use Psionic, Spell-Like, and Supernatural abilities more efficiently than the classic Series Helms wouild also be a good thing to include, given the inclusion of psychic player classes in the SRD, and the numerous OGC or not but official base classes with such abilities like the Hexblade and Warlock, and the ability to add 'monster' races at will via Savage Species. Ki users, too, for Monks and Ninja. Some kind of standard and thresholds for the strength of such more esoteric abilities would need to be worked out, though... Major abilities would be the focus of the class, like the Warlock or Shadow Caster from the Tome of Magic, equal to a full caster, while the Hexblade is Moderate, effectively a partial caster like a Ranger or Paladin, and Monks and Ninja would be Minor. Maybe if they just added TR 3, 2, or 1 in a Series helm, respectively?
Another option to consider is making Spelljamming Speed a little less uniform - maybe standardize it on TR2, as the speed of the Furnaces that are the oldest type of helm, with TR1 meaning you have twice the travel time but TR3+ being a more gradual increase, maybe by 20% or 25% per TR. Thus the captain of a particularly fast ship, capable of making trips in half the time, can brag that his baby "can make .5 past cruise" (TR5 or 4 by the above) when he's haggling with a prospective passenger with an urgent need to be elsewhere while avoiding official entanglements.
Alternately, perhaps it could be "Make five past cruise" where he's proclaiming the ability to hit a triumphant TR7.
I think the Spider Moon write up had one good idea in extending the Size Category chart and giving ships an offset on it, but rather than bringing the standard ncategory names into it just call them Ship Class 1, 2, 3, etc. or by letters, or even by roman numerals or Boat/Launch/Cutter/Yacht/etc. up to Dreadnaught if that's what floats your coracle. Letting any magic user with Fly or Create Helm and Craft Wonderous Item make a helm if they want, at a price and required caster level based on how big a ship can be moved, is also fine with me - varient propulsion sources like magic oars, rudders, or sails, or Levistones and whatever too - just let the Arcane make better ones. Oh, and don't forget the Kliklikak's phlogiston ramjet drive, that was a cool idea even if it's only Insectare ships that use it.
Switching topics again, while thinking about those attacks at -20 to hit at one ship hex range (and I really disliked 3e's square based maps all along, I have to say) don't forget the AC penalty a ship, or even part of a ship like the sails or a mounted weapon, is going to have from its size. Even so, I wouldn't balk at letting ranged weapons have double-size range increments in zero gravity, once the character throwing or shooting has had a handful of shots to get used to it. I think smoke powder weapons (pistols up to 10 pounders at least) should be if not totally replaced then generally supplanted by enchanted weapons using the Launch Bolt and Launch Item cantrips, for the sake of preserving one's air envelope. Except, blast it, I don't think those are OGC spells - I know they're included in the 3.5e Spell Compendium, which was produced after WotC had abandoned OGC, but I don't know the original sources. Even so, a good low-level Force or motion-based spell can probably be found or even created to fill the role of "magically propel something light enough to hold in one hand to Long range" without actually copying them outright. Being a 0-level spell is good for cost-effectiveness, though I'm not sure on the price of charges of smoke powder versus charges of a 0-level charged item. Giff would probably still shun them in favor of actual smoke powder weapons, but everyone knows Giff are mad anyway.
I'm going to reccomend a System Display map with a third Inner System sized disk for showing lunar orbits when a ship gets into a planet's space, with each lunar orbital position equalling 60,000 miles, or one minute at cruising speed. This allows for an intermediate level of orbital maneuvering without going to the tactical map as such. I've created a poster sized vector art design for one, light grey on white for ease of printing, but don't really know what I'm doing with vector art nor have much familiarity in OpenOffice's drawing package so I haven't managed to actually print a copy. It also has a few eliptical/cometary orbits shown for those objects that don't follow a mostly circular orbital track. Advice o getting it out of my computer onto hardcopy, or just into a multi-Letter-page PDF format would be appreciated.
This has gotten a bit long, so i think I'll start a new one for my one largely-complete Spelljammer conversion, a monster class for Bionoids.