Perhaps introduce the concept of D-mods that are resistant to restoration, or a special suite of D-mods that are particularly nasty and costly to remove. Hell, introduce more D-mods in general, I'd say. Pristine ships are supposed to be noticeably good, yes? I mean, I%u2019ll note that ships tend to get somewhat stingy amounts of OP; what if you pumped up the base OP on all of 'em, but then D-mods cut into OP, or if there was an OP reducing D-mod?
I particularly like this. D mods aren't enough of a penalty IMHO, you can easily remove them and perfect ships aren't exactly rare. Make D mods more ubiquitous and OP reducing and the mechanic becomes worth it. I also like the idea of having a proficiency in salvaging and not just RNG. Oh you found a paragon floating in deep space? Well, you can take it but it has 8 Dmods because you suck. Likewise a player investing heavily in salvage tech (For want of a better term) can make a living by flipping ships they've found.