Carriers, and their escorts.
Pre-war and early war ships.
Scouts, maulers, and drone ships.
I hate PFs, but PFs and PFTs for completeness.
The Lyrans and Hydrans (did we really need the Seltorians and NTs before we got these guys?)
More generally, everything included in an unexpanded game of F&E. (And then start adding the expansions.)
Most of all, the single thing I'd most like to see, period, is an F&E-oriented Starmada Fleet Ops supplement with conversions for all the ships in the basic game, conversion notes from KA/RA/AA/..., any adaptations back and forth to F&E (for example, crippled vs. non-crippled in both games aligns very well, but how do you deal with damage to a carrier group?), and so forth. Fleet Ops looks like it plays fast enough that you ought to be able to finish a battle almost as quickly in it as you could in the vanilla F&E combat system, and it still leaves open the possibility of using full Starmada (or FC or SFB) for smaller battles.