The one thing that always irritated me, is the fact that the MK II VHFs (Wraith, Nephtys, Guardian etc.) all have the very exact model of their original HF sister ship. I mean, these ships have massively boosted stats, I think it should be reflected in the design. I am not talking about completely remodelling and retexturing them, just take the original and change it a bit.
Unfortunately, these are the ONLY pictures I could salvage from a very old (but ingenious) mod called Nomad Revenge II 2.29 (maybe some guys know it). Every house VHF had a slight rework over their HF.
As you can see, the changes are small, but noticeable. Note that this is an example and might not suit your taste, just so you get a general idea of what I mean.
Note: This ship was not modelled by me and I do not take any credits for it. It is from a Freelancer Mod called Nomad Revenge 2.29