In my space opera games, I’ve made Player Characters work their way up to becoming the crew and/or owners of a starship. Each P.C. takes on an essential role — pilot/helm/astrogator, communications/diplomat, engineer/mechanic, captain/mission leader, medic/xenobiologist, etc. If there’s more than one pilot and the group ship is large enough, fighters can be launched to assist during combat.

In my most recent campaign, the adventurers worked their way up to being promoted by a space navy. The team commanded a task force of about a half-dozen ships. Depending on the mission or session, they could keep their current roles on the flagship of the small fleet, or they could take control of smaller ships and corresponding crews (in D&D terms, I suppose they reached “name level” or Lvl. 10).

Designing vessels, support staffs, and missions was fun, but the role-players eventually agreed that it was tough to manage so much over a longer period, so they reverted back to two ships with the ability to call on the others for support as needed. Still, it is possible….

The ones that have worked for us are mostly Mecha games. of the ones I’ve played with the group.
_Battletech_ – more of a minis approach in this one we did a Mechwarrior game for three months which was really wrapped around the boardgame with down time and side events played in rpg mode. It was a blast.
We tried a similar thing with _Jovian chronicles_ but ship battles in that with players playing commanders using Lightning Strike was deadly.
_Aegis Project_ is possibly one of the best for integrated play (Mech and other types) really fun stuff and close enough to trad-rpg that its easy to pick up. .
_Remnants_ is a truly excellent trad-rpg as is _Warbirds_ (I prefer the WWII setting a’la Achtung Cthulhu style) we have had short sessions of each and these campaigns are technically both still running.
_Mecha_ by Chris Perin is solid too. You could very easily use them as “Ship” rules, I’ve used them as Tanshuman “sleeve” rules with out really a hack.
_Mechton Zeta_ is good with Starblade Battalion setting making it even better. Although it didn’t last long I think we had maybe four sessions I really wish the GM would pick it up again.
The rules for Warstriders in Exalted work in a fun way and I found it easy to run.

Ship rules I’ve used are _Traveller_ which honestly are meh YMMV.

The rules in _Ashen Stars_ for ships are really playable and we had fun during Dead Rock Seven with the rules. So much so we had more space battles than strictly necessary.

We are about to start a Firefly game and the ship rules are very flavorful again and you could easily have the players running their own ship each particularly if you adopted the cortex plus “pathway” rules there you make the milieu by connecting the players to the relationships with People,places and objects in the setting which you make up with rules – you could actually do this simply using these rules the game is not Trad-rpg really because it would be all about the way you “feel” about things and the melodrama pursuing your goals creates. Sounds fun to me.

Let me turn your question upside down for a second…

You have this exact same problem with fantasy games, and you probably just don’t know it.

Is everyone in your party a war-horse riding knight? maybe a few mounted-archer and/or mongol types?

or are some of them riding in the cart/wagon, while a non-knight drives the cart/wagon?

Or, do you not really care, because the plot rarely involves horse-mounted and cart-mounted fights? So, when they come up, you sort of wing it a little, and just don’t let that happen very often? The rest of the time, the plot happens away from these moments of travel … even though they still happen just like space ship travel happens in a space opera. Just because it happens, doesn’t mean it has to be part of the plot time.

The answer to how you handle this with fantasy games is, IMO, exactly the same as how you handle it with space ship games.

Everyone on their own horse is exactly the same as everyone in their own space ship… yet, no one complains that everyone in a fantasy game probably has some amount of horsemanship and/or cart-driving skill. So, why would they complain about everyone having at least a basic level of spacecraft piloting skill, in a space opera game? (show me a character in Star Wars that they ever depict as unable to pilot a ship … or Star Trek, for that matter; some characters REALLY shine as pilots, but _everyone_ is a passable pilot … even Leia pilots the Falcon at least once, and she’s not depicted as being a pilot AT ALL; R2 does a little maneuvering of the X-Wing when Luke isn’t in it, but that might only be taxiing … C-3P0 is probably the only character depicted as completely unable to pilot anything)

Conversely, everyone riding in one wagon, with no one really paying attention to the details of that … is pretty much the same as everyone being a crew-member/passenger on a big space ship.

And, you can mix-and-match. Maybe PCs pair up as pilot+gunner, and the party is a flotilla of 1-3 person craft. A flotilla of patrol craft (big enough for their own bunks, galleys, and cargo, but not big enough to house the entire party at once). Maybe they can do rudimentary docking or shuttling between the craft.

Maybe it’s like Battle Of The Planets, where there’s a medium ship that has the FTL drive, lots of smaller 1-3 person craft that are light and heavy fighters (and/or a research/cargo shuttle), and they smaller craft dock to the medium craft for FTL jumps, sleeping quarters, etc. … they split up for battles, and they regroup for long distance travel and day-to-day life. Some PC’s stay on the medium craft to man several gun turrets, or to operate special equipment (sensors, tractor beams, etc.), while the others are on the smaller fighters (acting as pilots and gunners). You can also think of this model as being “flotilla of small fighting boats + 1 moderate sized tender ship.”

(in the Star Fleet Battles “Star Fleet Universe”, you would do the “1 flotilla of patrol craft” by spreading the PCs across a PF flotilla, of mixed PF types … maybe a leader, a scout, a fi-con, a few battle models, etc. … and then the “1 flotilla + tender” might be a partial PF flotilla + a Frigate or Police Corvette with PF-Tender modifications)

(and, you can make a similar comparison between pirate sailing ship games to “all PC’s are in one cart/wagon” and “all PC’s are in one big spaceship”, except the transition from gunnery to boarding is balanced a little differently with sailing ships vs space ships)

But, really, you’ve already solved this exact same problem in Fantasy games, and Pirate games … you just have to ask how you handle it in those games, and then see if you can apply that same solution.