Although the UEF sub is slightly outmatched against the Aeon sub, it has one redeeming factor: you can order it to surface (by pressing “Dive” or “D”) and it will add its deck laser to the equation. This is usually a spectacularly bad idea, as it makes you vulnerable to land fire, sacrificing the UEF’s armor advantage, but it can kill hovering Engineers if it needs to, which is nice.
The UEF frigate is not only for naval assaults (its armor makes it difficult to kill except with subs or bigger ships) but naval intelligence. It has radar and sonar, and the jamming makes it impossible to target UEF ships by radar. The anti-air is just for show, but at least a single bomber can’t wreck your ships.