It's true that smaller ships become less and less useful as the game progresses. Shields, combat sensors, ecm, and other goodies become more and more essential just for the ship to survive, and a frigate barely has room for these if it is going to have any weapons to defend itself with. But there are still a few missions that a frigate might perform in the mid game. Scouting is one. It can be an unarmed scout. Especially with a cloaking device, which can substitute for all the other defenses it would normally need. Smaller ships have one advantage over larger ships, they are CHEAPER.
So having frigates and destroyers fitted with cloaking devices and long range scanners to watch your enemies can be better than cruisers. Also, there might be a need for medical missions. If your planets develop plague, you have to send a ship with a medical bay to deal with it. A frigate can carry a medical bay as easily as a battleship, and it costs a lot less.
[This message has been edited by Baron Munchausen (edited 05 August 2000).]