Suggestions:
1) Asynchronous mosfet switching. Instead of switching all mosfets on and off at once for one massive pulse, hook the batteries up to the controller in 6 (number of pwm outputs on the ATMega168) isolated packs, and stagger their mosfet switching. Shouldn't that significantly reduce load on things like capacitors and diodes, reducing heat / loss?
2) Switch battery input between parallel and serial connections. Efficiency graphs from the Enertrac motor thread on endless sphere show that for every RPM, there is a most efficient voltage (related to Paul's great tests on the relationship between volts, amps, speed, and torque). So it would be nice if you could adjust the input voltage based on the motor RPMs, but doing it manually should still be useful. Battery packs could be hooked up to switch between, for example, 36v 40A, 72v 20A, and 144v 10a, by switching them from full parallel, to parallel / serial, to full serial. Implemented as a pair of banks of manual contactors? (Combining #1 and #2 should make for an interesting diagram.)
3) Why wouldn't running some capacitors across the motor terminals be useful for smoothing things out?
(Freaking long thread.)
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