@bstott,
I am using the Uno32 and the Diligent folks have done one hell of a good job in making it as compatible as they have. No, it is not the same, but neither is the Due that also claims to be "Arduino compatible". I would say the Uno32 and Max32 are closer to being "Adruino compatible" than the Due just because of the voltage levels. Most of the pins on the Uno32 are 5V tolerant, and the ones that are not have protection to make them 5V tolerant. I have also run into the issue of boards that work on the Uno do not work on the Uno32 because of interfacing differences. So for one particular board I tweaked the library which had assembler for both the AVR and PIC chipsets. One I tweaked some things and remapped the pins it worked fine. So there are going to be some growing pains for those things, but I also see vendors creating shields just for the Uno32 and Max32. So that won't be an issue down the road.
BTW, if you don't like the way they did things you have the source code and firmware and you could show them "How to do it right." I am thinking of walking this path by making a plugin DIP version of the Uno32 that replaces the processor on existing Uno boards. This would allow people to upgrade their Unos to a 40Mhz processor and if I do the hardware right, work with most shields. There is already firmware hooks to allow such variants in the IDE from Diligent. You just basically redefine the pinouts in a config file. They also already have support for the DIP versions of the chips from Microchip of the processor used in the Uno32. They just run at 40Mhz, but some have USBOTG.