The Australian, the only man to win a world title with the Desmosedici, said the key to unlocking the bike's potential was to forego pride and adapt to the bike's characteristics.
Speaking ahead of this weekend's Indianapolis GP, Stoner said Rossi's struggles to do so made it logical for him to return to Yamaha.
"People have been saying for years one rider's style is similar to another rider's style and suit the Ducati. But I think it's nothing to do with style. It's pride, personally," he explained.
"However you think a bike should be ridden, you basically have to ride it how it wants to be ridden. You know, you can go to other manufacturers and say that's how I did it here and it worked, and why isn't it working there?
"But I think it's just about pride, and you need to give that up and ride it the way it needs to be."
Asked whether he was surprised by Rossi's switch, Stoner replied: "No. I think, you know, after two years like this it must be difficult, must be a little bit embarrassing.
"So I think it's going to be interesting to see what happens next year, but no, it's not a strange decision after two seasons like this; it's got to be difficult.
"He needs to understand if he's competitive again. So it's better to try and be competitive again on something which you know he's competitive."
Asked about his own success with Ducati, Stoner added: "But I think what we did with Ducati was great, but it wasn't just me. It was my team, my team-mates, everybody that's helped and actually put a lot of input in toward that bike.
"So it's disappointing to see the results they're getting at the moment, but I hope to see them bounce back soon."