If you break ships down based on how many pts you spend vs how many weapons/hull/shields you get, they're all pretty similar within each fleet list.
The differences are sometimes speed, turning, agility, command.
I would say its pretty common to have 1-2 ships with command+1
After that, it just depends on what you want to field, I've heard some interesting things about a flank of 2-3 'fast' ships going all power to engines to get around the enemy. Then some people like to keep 2-3 'agile' ships to counter-maneuver any agile ships on the enemy fleet.
We've only gone up to 1,000 points here so far, but we dont have any big number of miniatures, we've mainly been using tokens for ships that we dont have, and those things are too easy to shuffle around on the board so we havent used many more than that for the sake of keeping a track of everything.