Disclaimer: I have no experience porting a rotary engine - I do have a bit of experience modeling volumetric efficiency with cam timing on a piston engine and have a firm grasp of the physics involved
I've always thought it'd be a good idea to just slightly port the primary ports, mainly for a little bit of flow so you only lose a little bit of low end & idle stability due to lower primary velocity, but to go a bit more wild, like a large street port or a bridge on the secondaries of a 6-port so that once they open up (and keeping the vacuum or solenoid actuators to only switch them at high RPM, maybe with one of the aftermarket Vtec controllers), the engine really wakes up has seemed very appealing. That way you keep the idle & low-speed drivability for the most part (you lose a little compression ratio if you change the secondary closing timing), but get a lot more up top. Also, playing with the shape of the exhaust opening could be cool to allow a slower opening & play with the exhaust sound.
Anyhow, go for it! Experimentation is fun!