I am not sure if this has been suggested before however. What about different factions having different ship speeds. And the different ship classes of that faction having different ship speeds.
E.g. Liberty/Civillian lighter ships would be fastest in game where as BW/Rhineland ships would be slower as they have more armour and firepower meaning there is less power for the engines.
Or one thing i have seen before is an engine that speed increases or decreases depending on what ship you have e.g.
patriot - low mass, light shields and weapons means that this can achieve high speed.
However,
Liberator - Heavier than the patriot due to larger powerplant and cargo hold. It also equips better Weapons and shields (which would wiegh more) so that it has a speed when fully equipped slower than patriot.
I feel this would stop the fascination of VHF's and people would use different ships depending on thier flying style. It would also make 1.0 ships useful again.