I tend to find that there are a lot of mod ships that do better with vanilla weapons, where the mod weapons side grade or down grade in effectiveness if not requiring the stats of the mods ships to work very well at all.
Wanzers from DA work great in Drovers, although what doesn't? ORA ships also work very well with vanilla energy weapons, so much so that they have a built-in hull mod to nerf beams, and honestly only discourage them by a very minor amount.
If anything I'd say most mod weapons are kinda terrible and let their host ships down where otherwise they are just as good if not better then their vanilla counterparts. There are many small ballistic PD weapons or medium energy weapons n these mods that are rarely, if ever, worth using over their vanilla versions which isn't necessarily bad. Options are options, but usually they are more flash then result. Usually fighters and bombers from these mods are often just as good if not BROKENLY fantastic in comparison. But that might just be SS in general right now where it's hard to even design a bad fighter-bomber due to AI distracting being worth it's time in gold.
It is my opinion that, other then boss fight mods like the templars (one day I'll play with them, one day), any ship selection with as much good as it has crud like the vanilla ships is basically good enough. Yeah I might not use all the ships from a faction mod, but I don't use all the ships from vanilla either, so fairs fair.
Out of the faction mods I have played enough with to have a reasonable judge of them:
Diable Avionics: What they lack in cruisers and super carriers they make up with in Wanzers and that one transforming frigate that is VERY good in my opinion. A good match for the PL in mid size carrier spamming, but unable to compete with TT phase/super carrier shenanigans or Hege gunboat superiority.
LEGACY OF ARKGNEISIS: Anarakis Reparations Society or whoever they are. Might be a little unfair to comment on as I never really got around to using most of their fleet (and and older version of the mod), but they seem to be nimble, fast and relying on EMP weapons to match their more direct counterparts. They have longer range weapons then vanilla, but aren't as efficient in a brawl. They have a mix of disposable fighter drones, elite fighter interceptors and frigging gunboats for strike craft, a nice deadly mix but possibly missing the edge they might need to fully contend for a carrier based fleet. I'd rate them as sub par, but they were never contending for galactic domination anyway.
Mayasuran Navy: Imagine making the PL better. Yeah, now they can contend with Hege gunboat superiority and they have lot of new additions to their standard carrier fleet. I haven't played with the version that ads the new phase ships, so no idea how they match up to the TT in that field. Basically better all round.
Outer Rim Alliance: Broadsiding is hard for the AI to do, and with energy weapons it's even harder. But these are some of the tankiest SOB's in the sector. Their battleship struggles to use all of it's large energy slots effectively, the weapon groups or something like that, so I turned it into something that not even an AI radiant can kill. They are darn near unkillable without heavy carrier support. But they are also slow, so can almost never flee from combat if things do turn sour. Their weapons are strange and can have some utility options but I didn't favour them over vanilla weapons, which I believe they also use in their fleets anyway. Their fighters are like their cruisers, big, tanky, slow-er but packing EMP's at almost all times. They don't pack as much of a punch, but reaching that critical mass where you simply can never get rid of them is MUCH easier if they enemy don't just fire their main guns at them, which they inevitably will. I don't think they can match PL carrier spamming, nor TT in phase/super carrier shenanigans but can certainly match Hege gunboat superiority pound for pound.
Sanguinary Anarchistic Defectors: Strange faction that spend more on pimping their rides then building highly effective weapons. I'll say that they can be alright, but their default weapons are nothing impressive over vanilla energy weapons. Mass EMP fighter spam though, which is nice. I wouldn't put them up to matching any of the big three vanilla factions, but they are a remnant like faction to fight rather then a local power. So fight to hunt for free survay data, which is odd but cool.
Scy: It's been a long time since I played with this mod so I'll just say this, arm your cruisers and battleships with super-charged pulse beams, and they will delete half the enemies fleets within a few minutes. Assuming it still applies, that weapon is brokenly powerful.
Shadowyards Reconstruction Authority: Another long time since, and I'm getting tired of writing this all. But carrier spammers, like the PL. Otherwise they have equivalent energy weapon gunboats like the TT and they never fare too well in a gunboat battle against those who are built for it like the Hege.