Ehhhhh. A whole NTF vs. Vasudans vs. Shivans would be good, except it just doesn't look very good. The GTVA has the Colossus, Hecate, and Hatshepshut as capital classes definitely in-game, however a valid point is do we need to fill up all the slots? The answer is YES! In my opinion, all the FS2 destroyers get moved to Sins capital-class, corvettes and cruisers to Sins cruisers, and fighters and bombers to individual Sins frigates.
After all, what is Freespace 2 without Myrmidons, Erinyes, Hercules Mk. II's, Basilisks, Dragons, and Maras all duking it out to pave the way for the Sekhmets, Medusae, Nephilim and Taurvi to drop their loads? If the devs would get rid of the hardcoded limits on ship build slots, then we could really have some fun with FS2 ships, because FS2 is all about fulfilling your thirst for massive ship battles without having to give George Lucas your money
But as to too many weapons, you are correct. The Myrmidon (when I fly it) has 6 Prometheus S cannons, a slot of Tornadoes, one of Trebuchets, and one of Rockeyes. An Erinyes has 8 Kayser cannons, Tornadoes, and Trebuchets. And your standard Perseus has Harpoons and Tornadoes, plus 4 of whatever is best, Prometheus S or Kaysers. Basically, FS2 has more weapons on a corvette than Sins has on a capital. A Deimos would rip a Kol to shreds, to say nothing of a Hecate.
To make a very long story short, it would be awesome, but lag would ensue as Sins tried to handle all of the beams from your Fenris strike wing hitting the enemy Ravana, not to mention your fighter cover and theirs, all blowing each other to hell. Believe me, I tried it in the Homeworld 2 FS2 mod, and a Hecate vs. a Ravana lagged like hell due to reasons stated above, namely Kaysers, Prometheus, and Shivan lasers all flying around from fighters, plus the cap ship confrontation itself, and the missiles from said fighters as well.