Im not sure if im the first to say this but im throwing my 2 cents in i think it would be neat to have a 4th ship class a flagship. You could only have 1 in a battle at a time and dont make em god like make em slower then the cruisers if thats possible and make em maybe 30-60% stronger slightly more weapon and standard slots then a cruiser and some nice bonuses. Mabye some special mods or just the same as a cruisers mods dont want to make em to strong.
Im not sure how it would work but I always have loved having a main flagship in any space themed game plus it could add some more depth.