Problem is that there is a weight diffferencial on the motors, so they are definitely not using the same amount of power, unless of course, you have the Miata of the bike world with 50/50 weight distribution.
I have a single speed so I don't have a shifter, which obviously gives me more room on the handlebars.
I see where you would have a problem...
Here's the thing to do..
Use only ONE throttle and split each of the wires off of that throttle and connect each set of wires to the separate controllers.
It WILL work with no problems whatsoever.
The reason I personally can't do that is because I have a cruise control for each motor which sets the throttle voltage in one position, which means I can't set the cruise separately.