You are correct on two scores: politics does make strange bedfellows. And that US and India should be closely aligned.
The latter is easier said than done - you only have to look at the posts on this thread to see the residual amount of bitterness from the cold war on both sides.
Regarding the former, because Pakistan helped US till 1991, the US should support a dictatorship teetering on the brink of Islamic fundamentalism with nukes, a country that helped create 9/11, and a country that most hates the US.
Ah, yes, politics does make strange bedfellows..............
cheers
Either way, we need to align ourselves much more closely with India and display the national commitment and will to do so...meaning maintaining the effort across various administrations so they know we are not going to be fickle and turn on a dime.