i recently started playing again and unlocked both around the same time, i made the omega, noticed how lackluster if felt compared to mk xii quantum and tried to the Rom Hyp.
Omega's recharge after specials is silly since the normals are just light damage anyway. biggest reason i felt they weren't worth keeping the set bonus, which is really they're only advantage (if you don't have heavy fleet stacked stuff yet) compared to regular torpedoes that just shoot. the rom set bonuses... considering the 2 set for more dots, but this seems more of a beam boat kind of set, so that puts the hyper plasma as a set-less item for me.
i find it to be better burst than quatum during a charge on the target as i can out run the first set and fire a 2nd set that will all hit together placing 6 plasma dots on them too vs holding off till the 2nd set for fast torpedoes as the first wave would hit shields.
on a new toon building up a end game ship for the first time, elite cubes are much more doable for me with the romulan plasma than other options. if feels like a solid part of my growing kit.
it would be crazy to assume you should have one layout of items/boff/doff for every encounter. you should have the rapid firing items for rapidly approaching enemies and the big hit items for big health enemies.
and if you overgear the encounter, don't nerf the equipment the hard grind gets you... ask for newer and harder encounters!