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Car Tax: cars registered before 1st March 2001 are rated on engine size, not 'greenness' - under 1549cc is £135 per year.
'Free' servicing: the servicing is not free, it is factored in to the price (and profit margin) of the dealer. It also ties you into that dealer for three years, meaning you lose the benefit if you move a significant distance away. Also, it will not cover things out of the ordinary service schedule. Also, main dealers tend not to be the most dilligent of servicing garages; quality independents can be cheaper and more thorough.
Worn tyres - I would hope that an individual would view the car when buying and assess the condition of the tyres - if it has four illegal tyres it's an opportunity to knock the buyer down £200 - that £500 car becomes £300.
MOT - £50 a year? It can be covered out of the £3500+ saved figure on the cost of the car. It's not even one tank of fuel. The annual tax figure (£135) is about two tanks of fuel-worth. Per year. Peanuts in terms of car running costs.
Rail season ticket? I'm sure £5345 is cheaper than a rail season ticket, but £1500 is cheaper than £5345. Buying an Aston Martin is cheaper than getting a helicopter charter everywhere. What's your point?
Buying at end of contract - the car is not sold 'under market value' as you have already the depreciation and admin fees (and finance company profit). Depending on condition, it may well be more expensive than market value - Skodas don't keep prices as well as VWs, one reason they make secondhand bargains. As well as paying the lump sum (which will have been harder to save for due to 3 years of payments above what the OP is paying now), there is a 'option to purchase' fee (god knows why) of £60 - not much, but it's more than the MOT would have cost, which I know is a big factor to you.
Crash protection - I think a £500, 2-tonne barge (with higher road tax, admittedly) will come off better in a collision with a Citigo. It may be new, but the laws of physics (particularly conservation of momentum) still apply.
Don't get me wrong, I'm not against new cars and I think the Citigo/Up!/Mii is a funky little car, but suggesting a new car to someone with a £500 budget is off the mark.