Man, you start off with a BoP that has many options for changing the looks and so forth and then you downgrade when you level up to a ship that you have virtually no control over how it looks.
by the by, I think that Cryptic could solve this problem easily.
Since the BoP(and this goes for other klink ships as well) is typically easily recognizable , then why not make it so that as you level up, you don't get one ship design that you are stuck with, but you get a bonus ship design to the one you already have? Obviously, this doesn't make sense with fed ships, since all their ships are so varied from tier to tier, but with klinks, you might actually be able to get away with this.
So, how about it? Excluding the B-Rel design (since it's in C-Store at end-game), you could have total customization in the Klingon faction without having to do too much work for it!