I agree that reducing restoration costs would also require a rarity adjustment on recovering ships. Otherwise there really isn't much of a point to things like a commission for military market access. Salvaging ships after a battle becomes the primary way to obtain ships. Market purchases would likely become secondary or even unattractive. That actually makes sense lore-wise and wouldn't be a bad thing gameplay-wise imo (the noob trap part of the current system is a bit problematic), but there would have to be other adjustments in certain areas of the campaign system. Otherwise they might just get ignored by most players.
One idea is to leverage the contacts system kind of like how early access to blueprints is supposed to work. Want to restore a battleship? You are going to have to be really good friends with a high ranking official to do that. Lore reason: Average restoration shops don't have the manpower or equipment and so you need access to military-grade restoration facilities, etc. Something like that could mitigate having to do things like increase ship costs between hullsizes or possibly even having to adjust recovery rarity.
I also could definitely imagine a scenario where a player could use story points to "buy" that relationship for a one-time restore - with the number of points needed scaling by the number of D-mods on the ship and its hullsize.
*EDIT* Just brainstorming based upon the above for complementing the idea with a player colonies mechanic:
Industry Building: Restoration Facilities
- Gives X more credits per month for restoration services to general colony traffic. (Behind the scenes and not actually removing anything from nearby npc fleets.)
- Grants small X bonus to player faction Ship Quality. (So npc player fleets theoretically have access.)
- Grants the player the ability to restore frigate and destroyer hulls and remove up to 2 D-mods at this colony (Restoration price is deducted from the colony's monthly income.)
Upgrades to:
Industry Building: Orbital Restoration Shipyard
- Requires X colony size or some other requirement?
- Gives original + X more credits per month for restoration services to general colony traffic. (Maybe gets more attention to the player from other factions whether good or bad?)
- Grants original + small X bonus to Ship Quality. (Representing the idea that cruisers and capitals can now also use this and smaller hullsizes can remove more D-mods.)
- Grants the player the ability to fully restore any hull at this colony at the cost of the restoration price being deducted from the colony's monthly income.
- Building this at the cost of an Industry slot combined with Corrupted Nanoforge get's a sizeable Ship Quality bonus? It could increase that item's usefulness in a niche way over pristine ones.
As far as an endgame timer...I'm all for it. Though, I hope that in the sandbox play, there are missions/events that trigger such endgame happenings (with giant disclaimers that say "POINT OF NO RETURN" or some such). Knowing you're living on borrowed time does...motivate...certain playstyles and strategies. As long as it's an option, and not mandatory, I see no downside.
I generally like this method more than a "global timer until DOOM" sort of thing. Global timers can be really stressful in a RNG-filled sandbox. Then again, its optional so its less likely to matter overall.
Xcom did compartmentalization of difficulty pretty well. It was explicit when an action would noticeably increase either the campaign or average battle difficulty. I appreciated it because I could hold off until I got the new research I was working on or one of my soldiers recovered, etc. That was even despite a global timer on top of it, so maybe combining the two implementations like that would be interesting.