Weapon effectiveness cannot be compared cos there's no constant point of reference. But there is the speed of light. One faction travels way beyond speed of light. And the other cannot. That's all there is to it.
I'm not sure I'd say either use FTL as both cheat it. The Federation's warp is obviously far more accurate, reliable and safer and can pretty much drop into orbit than travelling around in hell. Possibly their most underrated weapon is the transporter though...
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Yeah I dunno what they are gonna do against a transporter. Like. Imperium has its teleportarium. But against like "Mr obrien, transport their entire bridge crew and hold them in stasis"?
Now as a matter energy convertor, void shield would... block it? But it's star trek. They will get over that.