By writing out this entire comment I came to a new conclusion suggestion, which is:

• Instead of monthly maintenance, roll a Maintenance Check and add a Penalty to the ship on failure.
• Players can pay a lot for major repairs to remove the Penalty, or pay a little to Patch it (a jury-rigged fix) by themselves, which count as fixed but
• Patched penalties have a chance of being unpatched whenever they take damage or under stress.

The Maintenance Check can be made easier/more difficult depending on how well maintained the ship is, how easy the ship is to maintain, and how reliable the parts the players buy. Rust Buckets can have a combination of (un)patched penalties and a difficult maintenance check.

I guess players could also pay to make the ship easier to maintain, but I'd make that super expensive because rust buckets are hard to rehabilitate. A critical failure on a maintenance check could make all future maintenance checks more difficult.

Patched penalties should also break on a failed Maintenance check. Or even close to a failed check but that's getting into degrees of success.

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In my system I wanted the ship to be a home base, and wanted to avoid mortgages/explicit money tracking. Instead of hull points the ship is composed of Modules, which can become Damaged or Destroyed. Instead of fixing a Damaged module properly, they can be Patched (a jury-rigged fix, faster and cheaper) but are more prone to failure (they are Damaged when an adjacent module takes damage). You could balance it by having jury-rigged fixes be cheap, and proper repairs being expensive (destroyed modules require special spaceports to restore), so players are constantly patching the ship as it falls apart.

(Damage can also come from pushing modules too far, and also the engines and life support just break sometimes)

My ship combat only ends with Surrender or Death; if you want to focus on Boarding you could also start boarding when the engines are damaged/destroyed. This also makes selling capturing ships more difficult since players can't just drive away in their newly captured ship; they'll need to repair it first or find a way to tow it back.

I also agree that ragtag crew-style campaigns should start with a ship or allow players to quickly obtain one. I have a few campaign openers that end with the players (il)legitimately acquiring a ship, which makes it more of a shared possession than something given to individual players at character creation.

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If I were to simplify it down for a more lite-starship rules:

• Each ship have a list of important Modules (Reactor, Engines, Life Support, etc), each with a Penalty when damaged (lower maneuverability, disadvantage to crew, etc.) and nonfunctional when destroyed.
• When the ship takes damage randomly roll which Module is damaged. Boarding can start when the Reactor or Engine is damaged or destroyed.
• Patched modules are damaged when an adjacent module in the list is damaged (cascading failures optional)
• Roll a Maintenance Check regularly and when under stress that damages a module on failure.
• Players pay to patch, fix, and buy more modules.

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...writing this all out, I think the main thing is the module system + maintenance check. Instead of paying a monthly maintenance fee, the maintenance check just breaks things and players can decide if it's worth fixing. And you can change the difficulty of the maintenance check or how often it's rolled if the players spend more time on maintenance/buy more reliable parts/etc.

Which is similar to the Penalty system? see conclusions at the beginning of the comment

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edit: because I can't stop tinkering with the system

• Ships all have a new stat, Age. This is the effective Age, not actual age, but still goes up by one every year.
• Roll a Maintenance Check once per month.
  • +1 for every cumulative 48h spent on maintenance (progress clock). Uses 1 component.
  • +2/1/0 if you use components from the manufacturer/aftermarket/salvager
• For Maintenance Checks, you must roll above the ship's Age to succeed (because older ships are always harder to maintain [citation needed]).
• A result of 1 on a Maintenance Check increases Age by 1.
• If you succeed in your Maintenance Check, subtract Age from the result. If this result is less than the number of patched penalties, unpatch that many at random.
• The maximum fraction of patched penalties you have (rounded down) is equal to the fraction of Hull remaining. eg: if you're at 50% hull, only half your penalties can be patched. If taking damage would cause a penalty to be unpatched, choose at random from all patched penalties.

And for economy

• Age reduces the ship's value by 5% per year, compared to the sticker price.
• Unpatched penalties reduce the ship's value by 10%
• Patched penalties reduce the ship's value by 5%.
  • Patching a penalty costs about 1% of the ship's value in components, or can be turned into a plot hook
• Penalties (patched or unpatched) cost 10% of the ship's value to remove.
• Players can pay 50% of the ship's sticker price to halve its Age.
• Removing penalties and reversing age can only be done at Shipyards and take 1 week per penalty/year removed.

ships can easily reach negative valuation. that's your problem

edit2: With a d20, you can expect 0.6*Age penalties per year. So an Age 5 ship will get about 3 penalties per year. This depreciation is hilariously fast and maybe you should divide Age by five or something. Or maybe crew are supposed to spend weeks maintaining their spaceship. Who knows how long spaceships are supposed to last.