After announcing his retirement at the end of this season, Stoner told the media at Le Mans on Thursday that he believed MotoGP was going 'backwards' in considering more production-based regulations.
However, although conceding that the field was no longer as competitive at the front as it once was, Rossi said that modern realities meant MotoGP could not simply chase rules without consideration for costs.
When asked about Stoner's feelings, Rossi said: "I agree in the sense that that's his opinion, but unfortunately you need to keep up with the times.
"It would be nicer for everyone to race with 25 prototype bikes in the field, but nobody has the money anymore.
"For me, riding the bike is still very enjoyable, like coming here and working with my team in order to do as well as possible. Lately the races are a bit less enjoyable compared to a few years ago, but I don't think it's down to the riders: I think it's more of a technical matter."
Stoner said in a frank explanation of his feelings that he had lost his passion for MotoGP because of the direction that the series was taking.
"It is not starting again from the beginning, it is going backwards," said Stoner, referring to the arrival of the production-based CRTs.
"For me it is not the championship I fell in love in. It is not the championship I always wanted to race in and, except for my competitors around me, they are the only ones who give respect for each other.
"Nobody else has enough respect for the people that do their jobs, working at the teams, working in the trucks, and putting this show on every week. It is not easy."