I've always thought that all ships should be Mk2. This means that all ships with Mk2 versions or already Mk2, remain the same, but Starfliers, Startrackers, Rhinos etc get boosted stats to match those of Mk2 ships, with no increase in value.
This means poor players remain poor, the ships don't gain any value, you still work up through to better ships.
Mk1 ships essentially become bad Mk2 ships, this means that players can take on Mk2 missions, the same ones that everyone else does, but their ship is sub-par in combat against other players. The ships would have slightly worse shields, energy and armour.
It's like a VHF with a HF shield and powerplant for example.