OK, now I know what the ideal controller is ;-) Let's hear what makes the ideal regen system.
It strikes me that the goals of the ideal system are (not necessarily in this order)
1- Recover the most energy possible
2- Integrate seamlessly into the riding experience
Starting with number 1 I think that means that you need super capacitors in the equation because the generator will be able to generate far more than the max charge capacity of the average battery. You'd either need the controller to "throw away" this extra current or somewhere else to store it. Hence the need for super caps. And, as pointed out elsewhere you'll need a way of stepping up the voltage output of the super caps to the system voltage. Sounds tricky and thus expensive. Is it better to just have the controller limit the max charge seen by the batteries?
With all the talk about battery balancing, if the charge is going back to the battery pack then I presume it would be most effective to use it as a "string charge" rather than a "bank charge". So, would this mean that battery balancers become more of a necessity?
For number 2, how best should the regen feature be controlled? Should it be entirely separate from the mechanical brakes? Or should it always be applied in tandem with the application of the brakes? If the latter, then should it be both brakes or just the rear brake? On a m/c you normally do the majority of the braking with the front brake (look at any production m/c and you'll see that it has far more braking power on the front wheel rather than the rear). Good m/c practice dictates that you always use both brakes - but I know a lot of people (me included) that often just use the front brake and only use the rear brake in emergency stop situations. I believe that some bikes have "brake balancing systems" whereby they always apply both brakes even when you only apply the front brake (normally bigger sports-tourer bikes).
The Vectrix goes for the complete separation of controls - but as Mik notes the two choices can interfere with each other. Especially because applying the front brake seems to not be very compatible with also using regen.
If I were to separate the controls I'd likely have left hand for the front brake, right hand for the rear brake and right foot for the regen feature (on an m/c with a gearbox right foot is rear brake).
If I were to have regen work in tandem with the brakes then ideally I think I'd have it set up whereby if just the front brake is applied then regen works at 50% capacity on the rear wheel (obviously). When I say 50% I mean that it would vary between 0 and 50% dependent on the amount of front brake applied. If the back brake was applied then I'd have it work at 100% capacity (varying between 0 and 100% based on amount of rear brake applied).
Do folks out there no how other bikes with regen are set up?