...Holdon, I sortof lied.
I named some ships by a system.
Engi B (the one that has one engi, correct me if i'm wrong) - Usually something making reference to the Master Sword from Zelda: Skyward Sword. Especially with Fi in it. (uss master, uss imprisonment, something along the lines of that.)
Mantis B - The Musketeer (named after cobalion, also the pokemon that inspired my username)
Crystal B (sorry if I spoiled it for you) - Something related to Yveltal (therefore i name my crystal a's something related to xerneas[uss life, sending volleys of pure death at enemies. how ironic.]), or related to King of Red Lions from Zelda: Wind Waker (guess what videogame series i like, but let's not go off topic)
This is sortof a spoiler, so I'll stick it in a spoiler tag...
...well nevermind, I don't know how to use spoiler tags. Will edit when I find out how.
"Remember, losing is part of the fun! ...No, I'm serious..."
The Engi was Shulk, one of the Lanius was Dunban and the other Reyn.
Later crew members were given names like Rikki, Melia, Fiora, Sharla and Dickson (although Otharon would have been a better choice).
Of course I to swapped out the crew a lot depending on who was better and changed the names to keep up with the Xenoblade theme.
I think I defeated the Flagship with a "Chain Attack" of lots of lasers at once.