The article DON'T USE ARDUINO (FOR PROFESSIONAL WORK) provides some thoughts on reasons not to use Arduino, including concepts on troubleshooting, licensing, and power utilization. All good reasons.
And the author did provide a couple of alternatives:
- Linux Gizmos: an unending supply of announcements
- arm mbed
- Lets Get Board talks about differences between three versions of Cortex architectures.
- STM32: I've heard about this a number of times
- Arduino's own list alternatives