It is curious fact in international politics that the two big democracies in the world, USA and India have been at odd with each other for most of the times. While there may be many reasons for this, one reason that I think is the differing temperament of the ruling classes of the two countries.
Historically, Indian elites love to speak of grand theories and high morals. But few of them actually practiced what they preached. Mahatma gandhi being the exception which proved the rule. On the other hand, the US ruling class were the pragmatic kind, preferring actions to pious words.
Hence, I think the Indians irritated the americans and vice versa. The americans found in Pakistani elite a more amenable lot. The pakistani too because of their middle-eastern historical links are also more of doers than preachers. So the americans found it much more convenient to work with the pakistanis rather than the highfalutin indian nobility.
But now things are a bit changing. The new generation of leaders (ironically filled with quite a lot of old people like Vajpayee, manmohan singh etc) have realized that lot of highsounding words dont count anything. And they are trying to put in motion a work oriented relationship. They realized that for india to be treated seriously in world affair, it should show some achievments rather than just the ability to talk and lecture a lot.
We live in interesting times!