I personally argue that results over a long career do count for a lot.
I have no doubt that without serious injury, Stoner would have won more championships. He was a fantastic rider while in MotoGP. You can't excuse, luck and circumstance your way into multiple championships without a lot of ability and talent. Neither can you have a lot of talent and application, and yet, excuse your way out of multiple championships despite multiple opportunities.
Like in any sport, competitors are getting better and better. Each rider is a product of his era, including the aliens of each era. Drop an alien from a previous era into a later or the current era, without the build-up, and he will be nowhere since the ingredients to success, i.e., the degree of training, attention to details and mental application are different and arguably tougher. More and more, riders/drivers are superspecialised in their respective category of racing since they have to give all their attention and energy to that series to maintain competitiveness.
Rossi gave some interesting insight into what it is like to ride competitively in MotoGP for so many years. He finds it a lot more challenging now, not simply because of his age and the challenges that go with it, but also, how much more is required of him in terms of race preparation, bike setup etc. to be competitive. All the riders have to do this. It's not that he alone has to be doing it to keep up with the bigger talents around him. What makes it even more challenging for him is to keep the motivation with all of this and to adapt to the tyres etc as they evolve, old habits dying hard when they no longer bring the results.
I do believe Rossi is getting more than his fair share of negative commentary. Yes, his attitude has sucked, especially as his competitiveness has declined. However, his success does say a lot
Dani is a great rider, no doubt. I agree that his size has likely been a disadvantage in MotoGP. However, each rider is what he is, i.e., complete and it's probably not a good thing to cherry pick a particular attribute and give it all the credit for successes or failures. We haven't considered the possible advantages to his size, such as fuel consumption, increased acceleration etc that goes with less weight.
At the end of the day, we look at results. That's why we use them and that's why we declare a champion over a season and not after a single race. This is why we declare a great over a career or after repeated demonstrations of success in different conditions, bikes, competitors etc.