The highest polluting drivers are not necessarily those with the vehicals that have the highest emmision levels but rather those that do the most carbon miles. It makes sense to link the cost of owning and driving a vehicle to the amount of miles driven rather than a yearly payment. It would be costly and un-enforcable to require drivers to declare their mileage for the purpose of tax however it would make sense to link the tax to the fuel they need to drive the vehicle.
Given the number of stations that now record the registration mark of a vehicle before dispensing fuel, it would also make sense to link the system to the Police ANPR records and check the status of the vehical for MOT and insurance purposes. If you fail the check you don't get fuel.
Linking the tax to fuel would also encourage business drivers to think more carefully about the miles they do, particulary if you require business users to declare mileage where it would be enforcable.