is there an advantage between normal weapons vs the faction versions of them?
example is Romulan plasma vs non named plasma
andorian phasers vs phasers.
is there any reason that I would want to have a faction weapon or non faction weapon over the other?
do faction ships (rom, fed, card. kdf etc) get a bonus for having one of their or other weapon types?
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In my personal opinion, Romulan plasma weapons are better than regular plasma but that's not because they are Romulan, it's because they have a chance to debuff damage resistance as well as cause DOT.
K'ymara, Orion Engineer. Caedera of Borg, Liberated Borg Tactical, Elyza Vix, Joined Trill Scientist. Christina Bellona, Augmented Human Tactical.
T'Lana, Vulcan Scientist. Arbol, Martian Tactical. Ayzer Bryn, Joined Trill Engineer. Hawke, Betazoid Scientist. Karna Valkras, Klingon Engineer. Beth Parker, Human Tactical
Sarel, Romulan Engineer (Federation). Yazuri, Reman Scientist (KDF)
Andorian phaser is literally just blue phaser, nothing else. The only restriction is that you need one of the andorian ships to buy them but all ships could use them if you had them. Though it's fed exlusive since fed-roms can't buy the andorian ships (T5).
As for the faction issue, dosen't matter. Some ships like the vet destroyers, phantom, mat'ha, gal-x, do profit from using their faction's siganture energy type but only because of their special consoles which do phaser, disruptor, plasma damage that is boosted by tac consoles. Aside from that there's nothing more to it.
Generally use whatever you want or whatever works best for your build, though you should avoid tetryon. It's proc is just useless.
In very broad terms, normal weapons get an extra mod while the special version of that weapon gets an extra proc or effect. In return, that special weapon gives up a mod. I'll use Plasma as an example:
A Very Rare Plasma Energy Weapon has only 1 proc, the Plasma burn. At the same rarity it can have up to 3 Mods like Acc, CritD, Dmg, etc.
A Very Rare Romulan Plasma Energy Weapon has 2 procs, the Disruptor Breach and Plasma Burn Procs. At the same rarity, will have 2 Mods.
There are some that twist that general rule like Spiral Wave Disruptors from the Galor.
Whether you go for the standard or special type is up to you because it's a game of give & take.
As for faction ships getting a bonus for favoring a type? Technically, no. A typical Fed ship has no built in bonus for Phasers, a KDF ship has no built in bonus for Disruptors, etc. However, there are certain ships that feature a weapon that is specific for that faction. A few examples:
Fed T5/T6 Galaxy-X: Phaser Spinal Lance (Built in)
KDF T5/T6 Guramba: Javelin (Disruptor; Built in)
Rom T6 Kolasi: Plasma Spinal Lance (Built in)
Fed T6 Phantom: Heavy Phaser Lance (Univ Console)
KDF T6 Matha Raptor: Heavy Disruptor Nose Cannon (Univ Console)
For the example ships, if you intend to feature those special weapons, it may be a good idea to specialize into that type. Do note however that I'm not sure if a generic +Beam or +Cannon tactical console will buff them. They may have a Universal Console that has a small bonus for that type. The Phantom's console has a Phaser bonus.
I think they only get boosts from the +[energy type] since they aren't "real" weapons but consoles and abilities that do [energy type] damage like the Tempest's phaser bomb.
"+Beam" (so probably "+Cannon" too) consoles work on Dreadnought Spinal Lances, use those on my Kara since the character had a set of upgraded Nanite Disruptor weapons available. Should be the same for all Lance type weapons (emphasis on should, probably worth testing the others out with a cheap console before shelling out for a full set of Vulnerability Locators or something :P).