The thought that the idea of creation of Pakistan was merely a last ditch effort, almost an afterthought, is way too much for most Pakisitanis to digest.
Anyway, I find Two Nation Theory pretty obnoxious primarily because of an unuttered notion that Islam, when in minority, is incompatible with Hinduism, being in majority, and can only be compatible in political sense, i.e. secular when the situation reverses, i.e. it (Islam) is in majority.
Jinnah's said in Lahore, March 1940:
'They are not religions in the strict sense of the word, but are, in fact, different and distinct social orders; and it is a dream that the Hindus and Muslims can ever evolve a common nationality; and this misconception of one Indian nation has gone far beyond the limits and is the cause of more of our troubles and will lead India to destruction if we fail to revise our notions in time. The Hindus and Muslims belong to two different religious philosophies, social customs, and literature. They neither intermarry nor interdine together, and indeed they belong to two different civilisations which are based mainly on conflicting ideas and conceptions. Their aspects on life, and of life, are different. It is quite clear that Hindus and Mussalmans derive their inspiration from different sources of history. They have different epics, their heroes are different, and different episode. Very often the hero of one is a foe of the other, and likewise their victories and defeats overlap. To yoke together two such nations under a single state, one as a numerical minority and the other as a majority, must lead to growing discontent, and final. destruction of any fabric that may be so built up for the government of such a state.'
Yet, the same gentleman said on 11 August, 1947:
'Now I think we should keep that in front of us as our ideal and you will find that in course of time Hindus would cease to be Hindus and Muslims would cease to be Muslims, not in the religious sense, because that is the personal faith of each individual, but in the political sense as citizens of the State'
I find these two speeches utterly confusing and at times, such as the two paras quoted above, even conflicting.