Ive had a few mx5's, and they all been very good cars but i have had a few niggles with them.
Have a very good look at the roof, it should be nice and supple, if its hard and dry it will need replacing before it cracks and leaks all over you, same for the rear window.If it looks new(the roof) make sure it been fitted right, around the parcel shelf there is a steel support that sanwiches the roof to the body check around it for any damp and a slight kink in the rear window means its not been fitted properly and the rain run off's might be letting water in. (- about 300-350 if it needs replacing )
Electric window cables can be a pain, and ive had one stick half way open, so make sure they are quite and smooth and they should be ok. ( - 100 )
Apart from the roof and windows which in all fairness get batterd every summer all mine have been great cars.