Can't really go wrong w/ the miata as a commuter car. As for a gas sipper, that depends on being easy w/ the right foot. I have the later 1.8L. Plenty of pep, just the gas milage can plummet if I spend alot of time flogging it above 5000rpm.
I would recomend finding a 95+ to get the 1.8 and higher likely hood for the LSD. the 99-05 (NB) is the 2nd gen. from 01 on is the more powerful 1.8. if u find the NB w/o sport brakes, usually special editions, 15" wheels are easier fits.
The plastic rear windows are on the NA body's first few years. Hard tops are interchangeable for fit, but those that have a rear defroster have different plugs depending on the year. Buy a miata that has the hard top is much simpler.