I went through this about 6 months ago and chose a mk3 MR2, and don't regret it one little bit. I thought it felt much more sporty than the mx5. It feels rather like driving a go-kart the road. The lack of storage could be an issue of it was your only car, but it's amazing how much you can get in the storage bins behind the seats and the front boot if packed well.
EVO tested it against the mx5 mgf Elise and boxster back in the day and it came out very well indeed links to scanned articles below