If your 30 mile motorway trip takes over an hour due to constant traffic jams and lots of stop starting, and your 3 mile trips take 20 minutes for the same reason, then petrol is the way to go.
If your 30 mile trip was a reasonably clear run, then a DPF won't suffer as it will get a chance to perform a regen, without you manually invoking it. To give you an idea of how frequently a regen occurs, I read my ECU this morning and mine's done 280 regens in nearly 8 years, which equates to one regen every 10days.
I have an old Mk2 6GH pre-facelift 2.2 diesel, which I've owned for three years and I've never had a major problem. And this is the 185bhp diesel that was supposed to be most susceptible to problems.
If you're not doing the high motorway miles and you're not looking for bags of low down grunt and in-gear acceleration, then petrol should be the preferred choice. The petrol engine has good linear power delivery and if you want more urgency, just like the MX5 - use the gears
Having driven both petrol and diesel versions of the Mk3, they are pretty good fun to drive and the philosophy of the MX5 runs through it, in that you don't need a 0 - 60 mph time of less than 5 seconds to have fun.
If you're looking for an auto box, I'm not sure whether the auto has changed much since its launch but I can vouch that the 2017 auto box is fine, and doesn't hunt like some of the Merc, BMW and VAG ones I've tried.