Sourav Ganguly was fearless and stubborn. He was aggressive and never feared about the media or other critics, whether it was his professional life or his personal life. Ganguly consistently gave opportunities to the (then) youngsters like Sehwag, Yuvraj and Harbhajan, even if they would fail on a more consistent basis. Many slammed Sourav for such decisions, but we all now know how good the players who grew under Ganguly's leadership have turned out. Had he not been firm on his decisions of giving good amount of opportunities to the youngsters, Indian cricket would have been in a huge mess now.
On the other hand there is a guy with the Midas touch, Mahendra Singh Dhoni. Agreed that he is a very good leader and has the ability to take the correct decisions when needed, but there is something that goes unnoticed. He lacks the fearlessness that Ganguly had. Dhoni fails to give opportunities to youngsters. Under Dhoni's captaincy, if a debutant fails in his first match and then in another one, he is OUT OF THE SQUAD! You can't analyze a player's class by one or two matches. Every newcomer should get at least one or two series to prove himself and not just a couple of matches. Even the likes of Sachin and Dravid fail sometimes, but that doesn't mean that they don't deserve to play cricket anymore.
Additionally, the guys who get the opportunities are by same means linked to his IPL side. Why was Manpreet Gony given a chance to play for India? Why is Saha given an opportunity now?
There are some guys who disagree with the fact of the CSK links, but even they know that when a player plays for CSK, his influence on Dhoni and the selectors is much more than someone else who plays better than him, but for some other team.
And Dhoni currently has a better side than Ganguly to lead, so its obvious that he will be more successful. Had Dhoni been the skipper of the Indian team when Ganguly was (in the early 2000s), he wouldn't have been as successful as he is today. Its the team which wins the matches and not the captain. A captain just acts as a catalyst and makes the way easier for his side, but the initiative comes from the players who are a part of his team.