After scoring two titles with Max Biaggi in 2010 and '12 and a further success in 2014 with Sylvain Guintoli, Aprilia gave up its works effort in the production-based championship in order to join MotoGP in an alliance with Gresini Racing.
Since then, it has never finished a race higher than sixth, and has been beaten by KTM to fifth place in the manufacturers' standings in each of the past three seasons.
In the meantime Kawasaki has dominated WSBK, with the Japanese manufacturer's lead rider Jonathan Rea having scored five titles in a row, while Aprilia has only been represented by customer teams with limited factory backing.
Melandri, who was a factory Aprilia rider in 2014 and stayed with the Noale marque for its switch to grand prix racing, thinks staying in WSBK would have been a wiser move.
"I don't understand it, Aprilia should have stayed in World Superbike," Melandri told Motorsport.com. "They should have fought for titles in Superbike.
"That was the perfect series for Aprilia. But the owner of the company didn't want that."