1. Ganguly went out on a high
This is precisely the issue - Ganguly has had 'high' series every now and then but at any given point of time, you had to make a call about he was in form or not. While on any given day, on any given pitch, you could expect a Sachin Tendulkar or Rahul Dravid to hold their own against ANY bowling attack, you could not do so with Ganguly with the same certainity. If anybody tries to argue against this proven fact, then I think that you are flogging a dead horse.
2. Ganguly did not bat up the order.
From I remember, Ganguly had all the batting spots (except for the No.4 spot, which typically has the team's best batsman coming in - The No.4 needs to be a natural strokeplayer and also have a sound technique so that he can be an asset when there is a platform already set or if the top 2 have fallen cheaply) for his taking - I remember he used to bat at No.3 but could not match Dravid's peerless technique in test cricket. So, given his talent/skill, temperament and technique, the only place that he could occupy was the No.5 coming in after Tendulkar.
3. Ganguly was the talent spotter / Captain Courageous
I honestly do not think that Ganguly turning up late for the toss against Steve Waugh was heroic or anything nice. Sledging while on the field is fine/okay - but being the Captain of the team and coming late for the toss - thats despicable. And for as much talent that Ganguly fostered, he killed as many. I think the ONLY reason that a moron called Yuvraj Singh (the biggest flat track bully in the circuit now). And he has been given such an assured run, that this guy has still not established himself in the test team - perhaps thinking of which model to hang out with next. Similarly, in terms of bowling, there was one player, named Murali Kartik whose career and confidence was wrecked, irrepairably. Not to forget Hemang Badani (who IMO was a better rounded player in terms of fielding, batting temperament and bowling). If I remember, there was this keeper called Saba Karim from Bengal who played with only one working eye, the only plausible reason being that he was from the same state as Ganguly. So actually doing a head count, objectively, either Ganguly is a no loss - no profit or a slight loss when it comes to nurturing new players. And if at all anything he has taught these kids, he has made these pseudo aggression like waving your shirt half naked (at LORDS for Godssake), talking crap and all that is cool. No wonder you seee Harbhajan Singh slapping Sreeshanth and others doing funny stuff.
4. Dhoni is a lucky player/crappier batsman than Ganguly
Perhaps true. Dhoni plays as if he is swatting flies. But I think Dhoni has a better temperament. I (and the whole world) can see that Dhoni has moved heaven and earth to improve his batting from what he was. True, he does not look elegant or stylish - but he gets the job done, and that, I believe is all that matters. And I'm certainly amused as to what people call as Luck/fluke. Every achievement by Dhoni is being attributed to his luck. I can accept or cede a point if Dhoni's successes are few and far spread. But how come a person can be SO lucky that every time when the game is in clutch, his decisions pay off? Come on, if Dhoni was so lucky, he should be playing the lotto everyday and very soon, Bill Gates might have a competitor for the World's richest tag. But again, the resources that Dhoni has and that Ganguly had were different. Ganguly got a losing team (from SRT) while Dhoni got a competitive unit from Dravid. So I do not think its a fair comparison between Dhoni and Ganguly. But definitely, Dhoni's successes are NOT because of luck, just from mathematical or logical perspective (one of those cases when logic and mathematics concur). But just by the fact that to support Ganguly, his fans need to berate/talk down on Dhoni (and sometimes, Dravid), tells me that they lack the proper ammunition. They have come to a gun battle with a knife.
Now I have questions for the Ganguly backers:
At any point of time, when Ganguly was in the team, he was a weak link in fielding. You could not even classify him as a safe fielder. How many times have you seen him run with the ball till the damned thing stops and then throw it back? How many times have you caught yourself chuckling when Ganguly berates another player in the team for a misfield? And now the game being highly competitive as it is, every run that you save, might save you the match. Not a point of team when you want to carry a fielding liability in the team. As much as you can score a 50 in match and contribute to the team, misfielding not only contributes to runs lost but also demoralizes the bowlers/other fielders.
2. Inability to fix technical flaws
From time immemorial Ganguly has had a weakness against short pitched bowling. At various points of time, SRT and Dravid have had their shortcomings exposed too. But where they went back to the basics and fixed their game, Ganguly with all his (lazy) royal blood took his place for granted. By the time he actually sought help (before the 2004 Aus Series), it was too little, too late. As a person involved in quality engineering, I do not see a sane reason for anybody not to continually improve their game so that they retain their edge.