Miata is using a new lighter-weight SkyActiv manual transmission for the ND. This seems to have compromised its strength, although the failure rate isn't astronomical. I'm sure it's a ding to Mazda's pride, however.
On the other hand, the 124 Spider uses the bulletproof tried-and-true manual transmission from the prior Miata NC generation. Fiat made the choice to use the older manual transmission because of the Multi-Air's extra torque. A very savvy move by Fiat.
The.AT is the same one that Mazda has used for 10 years on Miatas, and is very well liked by the hard-to-please Miata owners who have it.