For what it's worth - this is what I replaced my NA6 (1991) standard unit with.
Clarion CX609A - Double Din unit -
http://www.clarion.com/au/en/products/2 ... 21675.html
Has tuner, CD, Aux input (front), USB input (rear), Bluetooth (don't actually use this).
Colours (display, dials, buttons) are customisable so I have set them to a similar green as the dash display/old head unit.
Rear USB is good - have run this via extension under the centre console into the centre console cubby (armrest) and can connect iPod or iPhone to it - control the iPod/iPhone via head unit controls (I actually leave an iPod Nano connected all the time).
Sound is via Sony Speakers (cannot remember now model) and they are really good (especially compared to originals). Have purchased Polk Audio speakers a while ago to install but haven't gotten to yet (and the Sonys are pretty good so probably won't until they crap out).
Went for Double Din to maximise the hole in the dash. Also went for this unit as (I feel) it better fits the aesthetic of the NA6 rather than a flashy all-dancing unit. Managed to locate a bezel that fits nicely so it all looks stock and neat.
Don't think you can get that particular model anymore but similar can be had.
Also - if you are replacing a stock unit - do what I did - don't hack into the existing wiring loom (i.e. cut off connectors etc.) - I ended up buying connectors, pins etc. (Jaycar and other places) and wired the new head unit wires into connectors that I could plug into existing loom connectors. Neater and if ever decide to restore original it's easy.
Lots of info here and miata.net on wiring pinouts etc. to help.