Teh problems mentioned above are pretty much why I am working on the replacement bike for CrazyBike2, simply because useful suspension of a heavy wheel is difficult (so far seems impossible to me with what I have avaialble), and putting the motor in the frame driving the wheel via chain (or belt or whatever) is about the only way that works well to let the suspension do it's job properly.
Moving CB2's heavy hub out of the front suspension fork to the unsuspended rear let me test whether it makes a difference to the suspension operation, and it absolutely makes a huge difference on both big and small stuff, even with a crappy 50mm travel spring/elastomer Suntour M2000 fork.
Unfortunately it makes the already obscenely heavy rear end of the bike even worse on bumps and holes, but overall the bike still feels way better than it did. Adding suspension to this frame is possible but kinda pointless, as the frame itself twists too much for reliable chain drive--as tested with my original powerchair motor drives, either the motor chain or the pedal chain ends up jumping off pretty frequently, and often ends up destroying drivetrain parts.
That flexibility does also give me some suspension in the frame itself, though, which you don't really get in a regular bike design.
If there's any way for you to do it, I'd recommend sticking the motor in the frame and driving the wheel with a chain or belt, as it will allow the suspension to react as designed to bumps small and large. If the suspension is made to do it, it'll be able to--with the hub in there it can't really move fast enough to deal with things properly (inertia and all that).
Doesn't have to be anything other than a straight 1:1 left-side drive, doesn't need to go thru the derailer or bike gears....just taking your hub and moving it to the frame will probably fix the suspension problems, if the suspension was capable of doing what you want in the first place.
That you can test by loading up the frame itself with the same weight as the batteries, motor, you, cargo, etc., and riding pedal-only with it, using regualr bike wheels rather than the hubmotor wheel. If it now responds like you want, then it'll work once really setup that way.