The Yamaha ace, dubbed the Doctor for his cool and clinical planning and racing, credited the 22-year-old Australian as being perhaps the toughest opponent he has ever battled.
"I think Stoner next year will be back stronger again," Rossi, 29, said as he wrapped up his sixth premier-class title, and the first in three years, at the Japanese Grand Prix here on Sunday.
"So maybe he is the hardest rival I have ever had, more than (Sete) Gibernau and all the others I fought against in the past."
Gibernau was the main challenger for Rossi's crown until 2005. The Spanish firebrand retired when Stoner replaced him at Ducati for 2007. It was at Motegi that Stoner crushed Rossi's title hopes last year when the Australian finished sixth and the Italian dropped to 13th with brake trouble.
"Last year I was sorry that after so many successful years, some people thought Valentino was finished and Casey was the new Valentino," said Rossi.
But Rossi said that this year, "I rode the best of my career. I think 2009 will be even more difficult than this year. But first I want to finish this year and try to win the final three races."
In their latest duel here, Rossi overtook Stoner with 11 laps to go and beat him by 1.943 seconds, ending their battle for the title. Rossi gained an unbeatable 92-point lead with three more races remaining in the season.
Rossi's five-year reign in 500cc and MotoGP ended in 2006 when he lost to Nicky Hayden despite winning five races against two for the former US Superbike champion.
"As I said, until I stop riding a bike, my objective will always be to win," said Rossi. "There are many strong riders but of course I hope that in the future nobody will win like Valentino Rossi."
Rossi stopped Stoner's winning streak at the US GP in Laguna Seca on July 20. Stoner, starting from his fifth straight pole position, fought tail-to-nose with Rossi but he slid onto the gravel with nine laps to go and finished second.
