A new guide is up about Faction Ships and the acquisition thereof, written by Joshua Foiritain, covering most all relevant details to getting these ships through agent missions. Excerpt:

Faction ships can be compared to named items, they’re better then the T1 versions but can’t match the T2’s.
Basically they’re ‘named’ ships (Though some are better looking then T2 ships and have ‘unique’ models).

They’re generally considered collectors items rather then real ships, mainly because only the Named Battleships can out perform normal battleships in the battlefield. (Until T2 Battleships come out)
T2 Cruisers and Frigates will kick any faction ships ass.

This, and more, in our Guide Section!