I like some of the ideas to balance out individual ship choices. Particularly the rarity system, and giving out smaller ships as a method of making a given ship worth it's weight in FAP.
Rarity: I like this in particular because it means that I'm not going to see two <CENSORED> Bin'Taks on the field or five <CENSORED> G'Quans. It forces players to consider their options a bit more carefully (Unless you have no options like say the League, Shadows, Ancients, or Vorlons...). It forces people to figure out how to use choices they wouldn't have taken otherwise. However, I don't think rarity works well in pick-up games or tourneys. Where it would shine is the Campaign system. You say this ship, after the campaign has started, costs /this/ much RR to buy.
Escorts: Escorts would be a good thing. It would help balance out a /lot/ of ships, in my opinion. Several limitations I'd put on the escorts though. One, escorts should all be Patrol-level choices. Two, Patrol-level ships don't get escorts. Three, the bigger the ship is, the more likely it is to have multiple escorts. The escorts would be included in the ship's profile, saying as such "Escorts: 2 Tethys Patrol Boats" or whatever. (EDIT: That way the 'rules' changes are mostly behind the scenes.)