First of all the concept of Muslim brotherhood is from our Prophet (S.A.W) and secondly Pakistan was made for the Muslims of Subcontinent If Quaid e Azam had the same opinion about Ummah as yours there wouldnt be any partition.
Pakistan and the so called subcontinent are separate ideologies, and should not be mixed.
The subcontinent theory considers Pakistan and India to be linked, which is completely false because Pakistan's history and basis for nationhood is completely distinct from the modern country of India. If the subcontinent theory was correct, then modern Indians coming to Islam would make us one nation, which is a fools' concept and already proven wrong by the creation of Bangladesh.
The notion of muslims being the basis of the new state of Pakistan was the political reality of conditions on the ground, where ethnicity could not be easily used due to language and Pakistan's perceived multi ethnic identity, which is it self a British legal conception, as the Muslims of Punjab, Sindh, Baluchistan, Kashmir and indeed all of Afghan lands did not historically see each other as ethnically different, but only culturally. Of course, Indian origin Muslims were welcome to be part of this new nation, but were never the basis of it.
Punjab is probably the best example of this reality, where an even remotely ethnic identity simply does not exist.