I put together a Google Doc with a sortable list of all the current reputation and storyline gear for starships, in an effort to quantify some of the thoughts I've had over the years with regards to the utility of various sets. Everything but the cores page is done at this point. Feel free to have a look: https://docs.google.com/spreadsheets/d/1...sp=sharing
The document is organized by equipment type (deflectors, engines, cores, and shields) and is only for ship equipment sets right now. I may add weapons at a later date but I feel like that topic is pretty well quantified already, and additionally the weapon usage is strongly driven by whatever is "best" in the metagame at a given point. Ship gear on the other hand offers a bit more variety (outside of ICONIAN=DEEPS MODE), and in fact in many cases depending on your build there are some very strong non-reputation options to consider.
Most of the gear I have was at UR already except for a few of the shields and engines, but I do not believe that most items gain a significant boost in stats from rare to UR to Epic. Rather, the mods which are gained at UR and Epic drive the stat boosts, and in most cases I was able to account for these by looking up on stowiki or r/sto the ones which I didn't have yet.
The page is prefiltered and sortable, so if you're looking to maximize a particular stat or effect you can easily find what you need.