I've been reading on the XMEGA series, unfortunately they aren't terribly concise in their information (in their defense, the XMEGAs have much more hardware than the old MEGAs). The internal PLL claims 128MHz maximum output, but it isn't clear where this can be used (the AVR core itself seems to only be rated for 32MHz, when sufficient VDD is available). The timers also claim "extended resolution", but it isn't clear to me yet if this is automatically generated, or just more bits (and therefore only useful when the PLL is clocking them extra), or what.
There are devices out there which have internal delay or phase shift circuitry, which allows continuously variable (so to speak; i.e., limited by the internal DAC driving it) "fine" control, or at least additional (sub-clock) steps, for PWM or frequency or both. Those would be excellent for self contained control applications (motor control, or yes, even straight up switching supplies -- given suitably clean code, of course!).
Tim