its not about the captain, Dhoni has been one of the better captains of India, better than tendulkar and dravid anyway.
they just cant produce good fast bowlers. they say zaheer khan was missing a) its a sad day when a country's biggest hope is Zaheer Khan, a mediocre quickie and b) they were missing atleast 3 quality fast bowlers and a quality spinner. Harbajhan is not a good spinner, atleast in ODIs and atleast as far as Pakistan is concerned (dont really follow him otherwise).
as Manjrekar points out, this has been the story for 20 years. It is amazing that they can presume to think they're world number 1 with such a consistent incompetence in a vital part of the team.
Lame excuses as far as bowling goes for India. RP was regarded as their best pace option alongside Zaheer. Ishant Sharma was the next big thing last year. Few months they were saying that Harbhajhan Singh has found his lost touch once again.
The only poblem they had with the bowling was their idea of playing with 4 specialist bowlers. And it sounds really stupid if they are going to use this as an excuse. India is always known to prefer 7 batsmen and 4 bowlers in ODI's.