A lot of the more powerful mcus have much more advanced PWM capabilities than the rudimentary counters in the Arduino's ATMega provide. If you prefer to stick with 8-bit, Atmel's XMega parts have much more powerful timer/counter modules, and most of the major mcu makers also do several chips specifically designed for controlling power stages, such as Atmel's AT90PWM series. There are more options in the ARM realm as well, for instance I know Atmel's SAMD21 (Cortex M0+) series have what they call "Timer Counter for Control" modules with programmable fault inputs and things. I haven't used them for anything but basic PWM to date, but they seem reasonably powerful from the datasheet. I'm sure other ARM integrators have parts with similar if not superior features. Probably best to browse a few catalogs and skim the datasheets of the most likely parts to see which best suit your application.