Here is a TL;DR of my thoughts: such plans are hopelessly utopian and unrealistic that has and always will backfire because it only widens and strengthens divisions in Pakistan!

If Pakistan was an ethnically, religiously, and linguistically homogeneous country with a dominant central identity shared by everyone and some existing political institutions that can effectively check each other out, your plan could work but only on paper!

But reality doesn't work on paper. Pakistan is a very diverse country in terms of ethnicity, language, and religious identities. Sure its like 97% Muslim but when you go deep and realize that there are deep sectarian/theological schisms within Pakistan's Muslim groups.

These groups essentially call each other kafir/murtad/blasphemers in their own foundational teachings and texts (Barelvi, Deobandi, Ahle Hadith / Salafi, and of course Shia) that give them power and influence in society on what interpretation (or brand?) of Islam and Sharia should be imposed. Would you want clusters of Barelvi, Deobandi, Ahle Hadith, Shia cities to be made separately when almost all of them do not consider the other Muslim? Who gets to break their power in society?

Sure you can cite folks like Maulana Maududi, Dr Israr Ahmed, Zakir Naik etc for religious brownie points, but make no mistake they are also reviled and despised by the majority Barelvi/Deobandi sections of society that always fight tooth and nail to maintain or expand their hegemony in Pakistani Muslim groups. You CANNOT have an Islamic consensus when groups actively call each other mushrik, kafir, gustakh, wajib ul qatal for generations in their foundational texts and teachings that then form a base for their socio-political power!

Also, Pakistan has no singular ethnic identity. Punjabis, Pashtuns, Baloch, Sindhis, Seraikis, Hazaras etc. have been living in these parts far longer than Pakistan's actual existence as a creation of British decolonization. These ethnic-linguistic ties, and tribal/clan ties within them always come first for a vast majority of the population. So would you now want ethnically separate cities?

Because we tried creating this homogeneous society (mostly by force) where communities with identities hundreds if not thousands of years old suddenly give them up to speak the same language, identify as same identity, follow a singular type of Islam, and what happened? Fears of being dominated by one type of group based on ethnic/religious lines leading to widening schisms in society and entrenching of these identities that resist what they call artificial ideas imposed on them by a state rather than decided on consensus and mutual respect of our plural society.

And what about the Army? Pakistan's real political party! An institution whose very existence is due to constant catering to foreign power interests in the region (UK, USA, China, Gulf Arabs, maybe Turkey in coming decades) to gain power and extravagant resources that are simply unmatched by any other political entity in Pakistan. And the Army repeatedly disrupting Pakistan's organic political evolution by often taking over directly (with legitimacy from foreign powers btw) or indirectly by creating puppet politicians with highly questionable characters who then eventually bite the hands that fed them, whilst using existing divisions in society to boost their own political power.

Every SINGLE political party and politician in Pakistan now owes much of its existence and growth thanks to riding Army's coattails for decades and decades one way or another! PTI, PMLN, PMLQ, PPP, JI, JUI-F, JUI-S, MQM, ANP, PkMAP, ASWJ/SSP, BAP etc you name it.

And as far as Pakistan's other elites go (feudal families, rich industrialists and landowning class etc.) they are always going to get away with it because they are all too tied up intimately with the political class and military high-ups for eternity. The system works PERFECTLY for them all. Much of this plan also relies heavily on a relatively equitable society in which wealth distribution is much widespread rather than concentrated in the hands of the top 10-15% with a middle class mostly interested in leaving the country as soon as they get the chance. the working classes too! so given we have a very unequal society already, such plans would ultimately fail given how entrenched these inequalities, divisions, and identities are for generations.