The flagship i'm currently building barely uses armor at all (only for looks).
It simply won't need it, regular hull blocks with integrity fields work fine if they are big enough.
They only have to endure the occasional shield ignoring shots, cause my shields can pretty much ignore everything else. :D
And yes, especially front and back facing thrusters (to brake) are important.
They don't need to be super flat anymore (the beta branch changed that). I build my "thruster arrays" out of a bunch of medium sized cubes, mixing good surface area with volume.
PS:
Trinium really is your best friend, it's good for all purposes.
Xanium is can be better for shiny stuff (like generators) and Ogonite is best for armor, but you can never go wrong with trinium. :)