I wasn't really thinking of sinusoidal drive, but rather just using the SIN/COS sensors (whcih output their namesakes' waveforms for the positioning data) instead of typical 3-hall sensor setups.
Since the encoders on each motor would be differnet, it would probably require programmability for the relationship between the SIN/COS outputs and the alignment with the phases/stator teeth.
If there is programmability, then the hall sensor inputs could also be programmed to work as analog rather than digital in, if that's what's being used. If not, well, then another pair of analog inputs (or externally muxing the SIN/COS signals to use with a single analog input on the MCU) would be necessary. I dont' know if there are any unused pins on the MCU, much less if any that do exist are also analog inputs.
The STM8 is a neat little chip;http://www.st.com/internet/mcu/class/1738.jsp
I have one here in a USB stick, though I can't seem to get the hang of programming well enough to do anything with it beyond the downloadable demos and such. The STM32 would be really nice for a controller chip on ebike controllers, but I'm not aware of one that uses it.