I don't necessarily agree with Tom's opinion, power alone does not a sports car make and as such there can be no denying that the MX5 is a sports car. However, I have never really cared for labelling them either way as it is just opinions and snobbery.
The e89 is a lovely car to own, be it a 2.0 or 35iS, you will be happy, yes it is slightly heavier than the e85 but it is a better car by miles, less skittish and its only the electric steering that has my criticism, that and the standard stereo.
As for engines, my preference would be the 28i, economy and emissions are the same, resale values will be better as there are fewer of them and performance is better, however if it was a case of 2.0 or nothing the it would be the 2.0.
As for the 35i, it is half a second quicker to 60, but is considerably more expensive to run, the only real advantages over the 28i are the two extra cylinders and that DCT
Good luck