At the time, only 2 Cortex-M0 chips were on the market available in such a small package. One was the Nuvoton Mini54. The other was a chip from NXP. I seriously considered the NXP part, but nobody seemed to have stock and I couldn't even get a reliable quote with lead time for quantity from any distributor. The Nuvoton part was in stock (small qty) and they gave a competitive quote. Initially they gave a very long lead time, but later revised it to several weeks, which worked out well for the Teensy 3.0 release schedule.
So, between only 2 parts at the time (early 2012) that met the small size requirement, one that didn't seem to really exist, the choice to go with the Mini54 seemed pretty clear. Today many more parts exist, but if you want to understand the original design decision, you really have to understand what was available in late 2011 to early 2012, when Teensy 3.0 was originally designed.
Later this year, we're going to switch Teensy 3.1 to the same MKL02Z32 chip used on Teensy-LC.