[MrMin]

Either way the 540watts must be "eaten" when braking..in one second. I dont think 4s or 6s plays a big role in this. It is more to do with the internal resistance of the batteries and that affects voltage stability under load. Basically it is a matter of good or bad batteries.
parallel(4S): Internal resistance will be less if in parallel, so theoretically a parallel setup will help with braking, but more current has to flow, so more heat.
series(6s): Internal resistance will be more, but current flow less for same power. Braking will be worse, but with good batts it will be ok.

Band-aids -(With better batts you need not worry about this):
CAPS: You're going to need a 1-2 farad cap. to absorb that kind of energy 50v..That will be as big as your car!! or bigger. and very expensive. And then the voltage will probably be over 30v and goodbye to FET.
CLAMPING DIODES: TVS diodes are there for short bursts.. Power zeners will dissipate a few amps over longer periods of time, switch off rather slowly.. My hopes were on this method as its cheap. In order to sink the excess reverse current. I still think it has some merit.(sorry patrick!).
ACTIVE CLAMPING: Use a linear IC(based on comparitors) to clamp the excess load through a external power mosfet. There are some nice ones on the market to do this. I believe this will be the luxury solution, but more expensive than above solution.

It would be nice to store the energy than to throw it away, but what to do with it and where to store it?

Still - the mmm and your truck will last longer if you drive sensibly by being easy on the 100% gas and 100% brake... (You can set your xmitter to help you as well.)
For those that want to push it 120%, be prepared to buy more parts. (batts and drivetrain)


Remember that a loose connection or a battery disconnect during operation will be FATAL to your mmm.

I'm only thinking out aloud here, so dont go and do things and blame me for it.