MS was a great driver but had a huge car advantage for many years. Shown by the ability of the car to sit in 5th place until the others pitted, whack in 4 fast laps and even up leading.
The reason why he did this was because this was the cleanest method of overtaking. As you well know, overtaking a slower car is actually quite difficult and has its inherent risks. So, why bother taking these risks, when you know that when you get clean air, you can demostrate your overwhelming speed and overtake during the pit-stop sequence. I know it isnt very exciting, but it is effective.
An intelligent sportsman, analyses the game and its rules. He then puts together a strategy that enables him to win. MS and Ferrar/Bennetton, did this to ruthless effect.
There is a saying, "Don't hate the player, hate the game."
Had MS won 1-3 titles, it could be argued that he didnt have much input in winning the races/titles, but if you win 7 titles and break every record available...there can only be 1 conclusion.
IN 2005, Ferrari produced a dog of a car. And it was in this season, where MS drove to the limit of the Ferrari. When on the limit, MS was able to score 63% more points than his team-mate.
MS didn't need to have outright No.1 status to beat the likes of Irvine or Barrichello. He could've demolished them if he had to race them. However, it was team effort and to increase the likelihood of title wins, Ferrari used a No.1 and No.2 driver setup.
Renault (with Alonso), also operated this strategy and were rewared with 2005 and 2006 titles. McLaren have also now adopted this strategy, as it increases your chances of winning the title. There is nothing wrong with this.