From my basic understanding, turning the motor via the wheels will generate voltage, which goes to the wires. If I go with the simplest approach and do not disengage the wheel from the motor when being pulled, is it right to assume I'll need a stronger diode to keep the back-emf from hurting the rest of the circuit (and possibly a bigger resistor for LEDs or whatever down the line of the motor)?
Well, if you have a diode on the circuit then the motor wont be able to turn in the other direction...
Do you only want the motors to turn in one direction? If you have a motor controller you wont need diodes.
Using the motor as a generator looks like an awesome idea. Probably too much for my first iteration, but definitely something for the future. I couldn't figure out how to switch from motor to generator at the circuit level. Maybe like a transistor switch so if a high enough voltage from the motor, send to a battery charging control? Are y'all aware of any projects that have done something similar?
well, you could have a switch that takes the motors leads from the controller to the battery, quite simple...
The only problem with measuring the voltage on the motor leads is that there will be voltage when the motor is being run from the battery...