2010, Stoner only beat Hayden by a handful more points than Rossi did 2012. I'm pretty sure you'd choke if I said Rossi trounced Nick this year.
Always making excuses and over exaggerating to blow smoke up Casey's arse.
Again you select the year that suits your purpose...
2007 Stoner 1st Capirossi 7th 200 points behind
2008 Stoner 2nd Melandri 17th over 200 points behind
2009 Stoner 4th Hayden 13th over 100 points behind
2010 Stoner 4th Hayden 7th 60 points behind
2011 Stoner 1st Dovi 3rd over 100 pojts behind
On the whole, I'd call that comprehensivley beating your team mate. 2010, Stoner had a few crashes as we know, but was either leading or challenging when he had them (Valencia excepted) therefore trying to win. The lost points brought Hayden closer, that's all, he was nowhere near challenging him. That's the difference between your Rossi/Hayden and Stoner/Hayden comparison - Rossi was nowhere near the podium, let alone challenging for wins. Hayden was closer to him than he was Stoner in terms of race performance, not through Rossi crashing trying to win.
With respect to Hayden, I think we all know who the best rider was 2006
With respect to your argument about Pedrosa besting Stoner in 2012, it's funny how your criteria only applies to one rider. 2006 Hayden finished ahead of Rossi, Rossi having let the pressure get to him in the last race by throwing his bike down the road all by himself. Hayden kept his head together to stay on the track, beat Rossi in the race and to the title. Rossi no doubt was still distracted from from the previous race when he was beaten by Elias and whining about his dangerous riding.
By your logic of course