Your spot on, the Viral ships are weaker than the ships they are based on. The idea is more strenght through numbers (and extra firepower) however, i feel i dont have enough ships in those various missions - however the false sense of security will serve Uni-T well in the next set of missions.
Thats good to know - hopefully the last mission will give you that epic feeling
(hint to winning the last mission: Only Fools Can Win)
This is the only place i feel that the mod falls down, due to the various modules and weapons, it is possible to create the rare ultimate killer combination. One day, when i get some free time i will patch that last hole in the mod which will stop the player making that uber ship.
Thats good the know - The whole idea was to challange the player, not have the situation where their uber steamroller fleet will conqure all. The various ships / weapons were designed with a similar concept to Rock / paper / sissors . . however there are times when someone rocks up with a tactical nuke and it all goes out the window