Some ship ideas.
Lunar Republic vs Solar Empire (low/med/high tech style/design differences)
Lunar Republic as low-tech: You could make pony ships in the style of the low-tech hegemony and lore wise account for it as Luna having bin away for a 1000 years and finding that ship design has progressed from her old fleet which lies in either disrepair or have just bin restored and taking back into use.
Solar Empire as med/high-tech: Mid-tech ships would be the mainstay ships of the Solar Empire while high-tech ships are brand new designs.
Lunar Republic as high-tech: The return of Luna brings back old lunar magic lost to the past.
Independent as mid-tech: Independent unicorn ships or ships of other races find a balance between the two goddesses.
Solar Empire as low-tech: Celestia has grown old and her magic has to span across the great defense fleet which does not allow for the energy abundance of Luna's ships.
Pony racial castes.
Earth Pony as low-tech: Earth ponies having to do everything by hoof and with little magic of their own fit well for the low-tech ship style.
Pegasus as mid-tech: Pegasus ponies are more accustomed with flight and its mechanics as well as their military history, there ship designs show a balance between the pony ship designs.
Unicorn as high-tech: Unicorn ponies being the magic users fit well with the energy style of high-tech ships, as well as their relative frailty, their speed represents their aversion for combat.
Individual ship ideas.
Apple family carriers: Applejack, Macintosh.
Science vessel: Twilight Sparkle, Starswirl the bearded.
Fighter or fast Frigate: Rainbow Dash.
Capital ships: The three Princesses; Celestia, Luna and Candice.