The first boss is named Pendragon. It's named after the guy that successfully drove Rome out of England, and you face it in Albion, a location in England.
The boss of the second level "Old Gaul City" is named Vercingetorix. Vercingetorix is the name of of a warlord from Gaul who attacked the Roman Empire.
The boss of the third level "Palmyra Valley", Zenobia, is named after the queen of Palmyra.
The fifth stage, the staging area for the Secelian fleets on the Secelia/Seraphim side of the gate, is called Carthage. The boss is named Genseric. In real life, it was Genseric who led the Vandals to conquer northern Africa—and make Carthage their capital. Carthage is also presumably where the 3rd Fleet was sent off from. The flagship is called Hannibal, a general of Carthage.
Why the Downer Ending for 13-Ship Mode? If the fact that ship #13 is the weaker-than-all-the-preceding-ships prototype is anything to go by, you sent ALL your R-Grays off-Earth--leaving no-one able to stave off other Secelian fleets! You didn't think Hannibal was their only planet-killer, did you?! On the Genius Bonus side, this reflects the late Roman Empire's bad habit of sending the vast majority of their armies to protect/expand the frontiers, with only a skeleton army protecting Rome itself. Something people like Alaric (a former mercenary for Rome, so he already had a sense of how the military roads and the defenses of Rome proper were set up) took excellent advantage of.