If you want the specific set bonuses and add-ons of a set, go for those. But honestly, even Advanced level gear can be great for a ship. Elite shields for example are excellent at being insanely resilient over time; I hate them in PvP, but they are good.
Elite Deflectors reduce science power (including science captain powers) cooldowns by 10%. And it applies for everything.
Now Elite engines are 'meh' honestly. Elite space weapons...feds get phasers (no torpedoes) which can proc a shield heal. KDF gets disruptors (no torpedoes), which can proc a shield resistance debuff.
Romulan plasma weapons are nice because of their disruptor proc added on, so if you're looking at those for good, solid weapons, I recommend em.