yeah but usually those internal diode are just simply too slow...

I think we don't use the same rules of thumbs 1000uF/Amp here... maybe i'm wrong?

When you said.. Place a 25V 470uF elect Capacitor for the 12V on the motor.
you mean in parallel with the motor??? not sure if you really need it. And.. mmm, if it's not a not-polarized type, you may have some problem one day or another... If it's only on the Vdd rails then.. that's ok.

Across the driver i would suggest 10-47uF tantalum + 0.1 uF ceramic.

Enjoy! and great to know it solve most of the problem