Seriously. I want to know what kind of starship designer or half-baked engineer would have access to replication technlogy (actually fabrication technology, but that's another rant*) and didn't build it into every facet of the ship.

regenerating hullplating? cool. Regenerating critical structure? Awesome. Brig cells that seal off and have no exit because they're contained in six walls? klingons belt buckles need not apply. Need to isolate a contagion? yeah. Seal them off behind a bulkhead.

Intruders? make it so the only way you can move about the ship is your transporter system.

Fuel shortage? Well. you know you could have powered your ship with a singularity core, right? any old asteroid is fuel.

and you know what the best part is? all of that comes with the inherent ability to specialize. Analyze damage when regrowing hull and increase the hull plating thickness where you get hit. analyze wear and tear on components, and upgrade the ones that wear out the fastest. Do you spend your time sprinting from crisis to crisis? tweak the performance of the warp drive for sprints.

You need a new starship? fire a photon torpedo with a replication warhad into an asteroid. New base? bigger astroid.

*you want replicators? THIS IS HOW YOU GET REPLICATORS. replicators are things that make more of themselves. fabricators are things that make more of other things, and maybe also themselves.