Hmm, I’ve read answers to all of those questions I believe... But I can't remember what those answers was. But I’ll tell you what I think.
okay another inconsistencies, the sovereign always had quantum torpedoes, why in insurrection and in the initial exchange with the scimitar did they use photon torpedo’s? Quantum are 4x as strong! I mean if i was riker I would have wiped around and just unloaded the quantum magazine in the sona's ugly stretched face.
Maybe they where out of Quantum torpedoes? Maybe they where trying to save them for a sure hit kill? I mean, you don't just unload all your Quantum torpedo’s at an invisible target and hope to get lucky right? And besides, there where friendly cloaked Romulan ships around. (It's been a while since I saw the movie so I might be wrong about the Romulans cloaking) And in Insurrection, didn't they go up against a federation ship there? Because in that case they wouldn't wanna destroy that ship to much. And when they where attacked by the alien ships didn't they move through a nebula? Maybe the increased explosion power of the Quantum torpedo might have set something of.
and if the pulse phasers are so strong why are they not eqquiped on the prometheus, steamrunner, akira, saber, and all those other advanced combat intended cruisers? I mean they deal damage to a ships hull through the shields, it says so on like Ditl.org i think, anyways i remeber reading about it some where.
I don't know what to say about the beams but about the Pulse phaser: It's true that they do damage through the shields since the pulse phaser is essential an onion of phased energy. One layer gets destroyed at the shields while the rest of the energy can continue and harm the hull. But, to equip it to all the ships in Starfleet would severely lower their combat efficiency.
The Pulse phasers can only fired in the direction it's mounted while standard Phasers can fire in almost all directions. Sure, on the smaller ships the Pulse phaser would be a good choice since they can turn really fast and because of that they can aim the Pulse phaser easily.
But on the bigger ships that's just not possible. And to have both Pulse phasers and regular Phasers would do several things, less space to use for diplomacy and the like since almost all Starfleet ships are not made for combat but Exploration. Less energy to use on other systems. And less energy over all in battle.
Uh yea... something like that.