Muslims are one single nation/culture and are different from Hindus...well even Muslims couldnt live with Muslims...that officially compromised the TNT...or atleast the major part of that reasoning.
Hey don't get me wrongly that I want a United India...it can happen only over my dead body and I want Pak and BD to stay away from India..just saying that TNT no longer exists as Jinnah envisioned.
On the contrary if the Two Nation Theory implied that you can abuse, mistreat and even, allegedly, kill your own brethren and they'd still stick with you...then yes..the TNT, as you abbreviated it, really did blow up in our faces resoundingly. However, the TNT was anything but that; it was an expression of us, Muslims, that Islam is a lot more than just praying 5 times a day and that, it has an opinion on everything from social interactions to standards of propriety, from economics to jurisprudence etc. and that Muslims, should, accordingly be given the space to express themselves with respect to all of the above.
Islam enjoins us to pray, to fast, to give alms etc. but it also talks about evolving a system of Finance wherein Rib'ah is taken out of the equation, where laws are made in the light of our own traditions on jurisprudence and where propriety is differentiated from impropriety in the light of our collective consciousness or in other words Islam. And that right to express ourselves in a manner, we see, consistent with our socio-political-economic and legal belief system or Islam as we call it...was what the Two Nation Theory was all about !
One of the raison d'etre of Pakistan was the right to express ourselves; the others were the very visible fault lines that existed between the Hindus and the Muslims and the growing fear that Muslim polity would be stifled in a Westminster style democracy without any constitutional guarantees for the Muslims. And all of them combined led to the Struggle for Independence.
As for Bangladesh...if I'm not mistaken even in the latter stages of Mujib's Govt. he had started showing some acceptance for Islam as BD's dominant culture and, again if I'm not mistaken, during Zia's tenure this was accepted explicitly so. Hence the expression part of it was incorporated.
Furthermore, the Two Nation Theory is hardly confined to the Indian Subcontinent alone...Muslims in Bosnia, Kosovo, Chechneya (Forgive the Spellings) etc. were butchered just because they were Muslims and were, consequently, made pariahs by being declared 'the Others' even though they, by every definition, belonged to the same stock as the Serbs, the Croats and were, by Orthodox standards, as Islamic as George Carlin. So, my friend, this distinction has been there and we saw its ugly side in Bosnia where an imposed TNT led to a lot of bloodshed and we saw the good side of it in BD where the right to express didn't come at the expense of exclusivity with respect to other Non-Muslims citizens of the state.
P.S Israel, ironically, is another prime example of the TNT because they carved out a nation for themselves on the basis of religion and got national cohesion in spite of very diverse ethnic and linguistic backgrounds.
P.P.S If you ask me, the Pakistan of today is not Jinnah's Pakistan and a practical application, for a plethora of reasons, of the TNT in Pakistan remains very much elusive.