I think it's a better system than in the past. Those that can afford the >£40,000 car new pay the higher tax. Those that can only afford the older, less efficient, cars aren't forced to pay the higher rate of tax.
It shouldn't make it difficult to sell in 3 years time. In general, a £40,000 car will cost £20,000 in 3 years - an extra £620 tax over 2 years is insignificant compared to depreciation. Those for which £620 is an issue won't be on the market for a £20,000 car.