My experience suggests that you are better off with independent throttles. Having a common plenum with high overlap makes the engine not run so well at part throttle. I think it's because the exhaust reversion can go right up into the intake, pulled up by the vacuum from the other rotor, instead of stopping at the throttle plate.

One interesting thing is that I've noticed this effect even with street ported primaries and a stock EFI manifold. My fuel injection system does batch fire only, once per revolution. Both injectors fire at the same time, so one rotor gets it during the very start of the intake stroke and the other gets it towards the end.

With the stock EFI manifold, which shares a plenum for the primary ports, I would have to run cruise AFRs in the 13:1-12:1 range for the engine to run well. With ITBs *and full bridge ports* I can comfortably run 14-15:1 without lean misfire. My conclusion is that with the plenum manifold, one rotor was being starved of fuel by the other rotor because of reversion. Under full throttle it was no problem because there's less reversion.