You most definatly should be able to pick your flag ship if you got 2 ships of equel level... not sure about extra ablities... but at least for flavor...
Captain Cigarzincetten of the Flagship Marza Dreadnaught TDN Fluffy reporting for duty sir!
Although... it would be an intresting mod idea if you could give your flagship (lv 5+ only maybe) (pick one) infallable jumpdrive or immune to disables(ion bolt, phase out, and so forth[not armistise i would guess])... or 5% moar shield mitigation... or phase missles dont go through shields, or immune to negative buffs (vertigo, designate target, and so forth)... you know, just a little something that makes it slightly harder to kill (since capital ships seem to just die alot)