Research Points which give you a new ship give you a new gameplay experience. The ship can be outfitted multiple ways, along with having its own unique feel as a ship. The ships are fairly expensive in terms of Research Points because they unlock quite a lot of experience to play with.
Unique Upgrades are less expensive, but still provide a different gameplay experience. The ship you'd attached them to is limited in variety for that experience because it's got a slot locked in, but the UU should ideally provide a new way to play a ship you already own.