Passing control voltages to multiple isolated power supply channels
I think the MCU-per-channel approach is a good one, assuming you're simply setting static voltages and current limits. You could use opto-isolators or magnetic isolators and send data serially bidirectionally (such as fault data in the reverse direction). I would not necessarily limit thinking to UART-to-UART communication- it might make more sense to send the data via SPI, which could avoid the necessity of closely matched clock frequencies. In fact, with the right SPI DACs you might be able to pass the digital data directly without an MCU (at some loss in flexibility). 

Another possibility, which could be cheaper, would be to use PWM to send data, which could allow you to use a single MCU, if it had enough independent PWM channels. Then the isolated control circuitry could consist of not much more than a reference, a gate and a low pass filter.