How I would do refurbish Spelljammer?
First and foremost, make it a setting of its own; not a half-donkeyed way of connecting existing settings, with all the baggage that involves.
This means giving Spelljammer a tone of its own. I'd go with the 16th-16th-century vibe of pirates, explorers and so on; this would mean adding firearms and cannons (with possibly alchemical and magical versions as well), and getting rid of catapults on ships.
On the other hand, I'd emphasize the fantastic designs of the ships; more Mosquitos, fish-headed Merchantmen, Squidships and Nautiluses, and less longboats, caravels and other boring stuff that only existed because Spelljammer had to include a way for characters from established, non-Spelljamming worlds to get into the setting.
To go with that, refurbishing the ships is a must. The first problem with the existing helm system is that it requires a wizard to power it, and it makes that wizard useless for much anything else. Thus, you either need a NPC to power the ship, or one player to bear the burden.
The second problem is that the helms are way too portable, and very expensive compared to the hull of the ship; this leads to people looting the helms and leaving the hulls behind. Make the motive power come from the structure of the ship, instead; now, if you win a battle against an enemy ship, you have to either leave the ship behind or figure out a way to bring it along, instead of just looting a chair. (Again, I think the easy portability of the helms exists so that you can find one in a dungeon, bolt it into a ship, and fly away.)
And while we're at it, let's ditch all the weird helms that existed to get around the very limited availability of arcane spellcasting in AD&D. I'm not saying that there shouldn't be various drive methods around, just that those shouldn't exist because of the inability of the rules to handle a dwarf wizard.
Finally, I'd ruthlessly purge all the goofiness from the setting. Goofy is not the same as fun; most of the time, it isn't even funny in the long run. Thus for example, no wacky, goofy tinker gnomes (one of the worst aspects of Dragonlance, IMO) with cobbled-together ships powered by rubber bands and giant space hamsters; if you want to have gnomes, make them eccentric but competent engineers, more like Captain Nemo, Robur the Conqueror and so on.