It would be nice to be able to have more flexibility with weapons/hull mods.
What about increasing the logistics cost instead of reducing CR though? That way you'd have to choose between a smaller number of really good ships or a larger fleet of good ships.
Already in the suggestion, though I phrased it as "maintenance cost" rather than "logistics cost". Same intent, though.
Come to think of it, increasing the CR cost of deployment might be another reasonable notion; probably in addition to my original suggestion.
The positive influence of 50% more OP would far outweigh the lowered combat performance of having 50% less CR. At least as long as that doesn't bring you into the malfunction area, you'd just need 70% CR or more to stay above 20% CR. The tripled maintenance cost might work as a deterrent for big fleets, but small or solo fleets can easily spare those.
I'm not entirely sure of that - remember, reduced CR means less speed, less autofire accuracy, more damage taken, and fewer sequential deployments... it really does factor into everything. (Aside: Being able to *see* what bonuses / penalties your CR is giving you would be very nice, rather than just the "You're getting some bonuses from CR" status icon that's there now. Unless maybe there's a tooltip somewhere that I've failed to notice?)
Plus, I know my personal "small fleet" wouldn't be able to support 3x the logistics cost of my Apogee, let alone any capital ship. I'd probably go over by a bit - I can spare some amount of logistics capacity / max CR - but definitely not the full 50%; probably just enough to add some point defense. (Currently, my Apogee is armed with a plasma cannon and two phase beams; I just take missile hits on shields.) And I definitely wouldn't go over on any of my supporting frigates - they're there to chase down things that the Apogee can't, and reduced CR = reduced top speed.
Dunno. Might need some fine-tuning. But as you mentioned, I do like the notion in general, even if the details aren't quite right yet.