I don't think this question needs to be limited to motorcycles; in fact, when you consider the plight of the Wankel with respect to cars, it answers the question for other applications as well.
I believe the last great production rotary was in the Mazda RX-8, and stopped about 4 years ago.
Apex sealing has always been troublesome, especially on cold starts. Rotor lubrication was also always an issue, and the Suzuki RE-5 you mentioned had a system to pump oil into the trochoid chamber.
Heat has been a real issue since day one in the late 50s. The exhaust stays in the chamber for a long time, transferring the heat to the rotor and trochoid chambers. Because of the shape and geometry inherent with a Wankel, it's difficult to get cooling passages where they need to be. Cooling systems tend to be complex and problematic.
The ignition system is usually complex, consisting of a minimum of two spark plugs per rotor. The compressed area is a long chord, and because of its shape does not promote a single-point ignition with a resultant efficient flame front.
Emissions from a rotary are not easily controlled to today's exacting standards. This may not be so much of an issue for a motorcycle, but I believe it was a strong influence of the demise of the RX-8 in Europe.
The bottom line is something @TMN referred to: return on investment, and just a plain "Why?" Modern motorcycle engines are making in excess of 200hp/liter. With reciprocating 4-stroke pistons. Why would anyone even consider a Wankel-engined motorcycle, when 500cc and 750cc monster beasts, (quite tractable, meeting all emissions, excellent fuel economy, gobs of torque) ... are available at every Honda, Yamaha, and Kawasaki dealer around??
What seemingly made conceptual sense and promised 12A or 13B utopia in the seventies didn't come to fruition, whether for cars or motorcycles.