Which south asian empire? most empires where foreign conquerors. I dont think a south Asian empire is ever going to happen, especially considering that the movement for Pakistan and even Afghanistan refuted this concept and refused to relinquish their identity and recognized themselves both politically and historically as distinct and chose a path quite different from the South Asia. Even attempts to form economic/ trade blocs(eg. SAARC) have for the most part been failures and non-functional and in many respects impracticle. Even within india, many ethnic groups are resisting what they fear is the absorption of their distinct identity and culture. In the case of Pakistan, there are many problems being faced by the ''Mohajir-urdu'' ethnic group which still face problems of integration and acceptance into the social dynamics of the various ethnic groups inhabiting Pakistan, a problem that for the most part, Afghan refugees have not had, many have intermarried or joined into parent tribes. While newer refugees have been repatriated, the process has been difficult for the government which has opted to focus on those residing in refugee camps because those living outside are integrated for the most part and can be found in almost every corner of the country.
Furthermore, the relationship between the people from a historical point of view is different as well, as often Afghans and or Mughal empires, when it came to the region of South Asia, where areas conquered by invasion not under some common union.
As far as the Sikhs are concerned, they are relatively new entity from a historical point of view in that they are a reformist sect founded in the Panjab province after the 17th century and represent less than 3% of india's population and are also found in Pakistan, albeit in smaller numbers. They can be seen as transitional.
Also, it should be pointed out, that there are no Pashtuns in india, while many claim to Pashtun ancestry, this has been disproven by genetic studies and even by phenotypic expression. They neither look Pashtun, speak Pashto or have any cultural similarity to the Pashtuns and many where simply converts to Islam who opted to alter their surname to improve their social standing; perhaps as a result of the predominant caste based culture of india. They are not accepted by any of the parent tribes in the traditional Pashtun regions of Pakistan or Afghanistan. Also, many of the Mohajir-urdu people(s) of Pakistan who inhabit Karachi, a sizeable number also claim such lineages and despite living alongside an estimated 4 million Pashtuns are not considered Pashtun but urdu-speaking mohajirs even after 3 generations by all Pakistani's and Afghans alike. The majority still cant speak any of Pakistan's indigenous language(s).
Going back to the point of the thread, the border between Pakistan and Afghanistan has been quite difficult and infact impracticle to delineate, this is due to Cultural, linguistic and tribal ties across it(Many tribes simply act as if it doesnt exist) and also do to the topographic geography of it which makes it next to imposible to seperate the two countries. Even historically, many Afghans established reservoirs and colonies in the areas that now make up Pakistan, and Afghan families still inhabit areas of Karachi where they have lived for over a hundred years (eg. Logar colonies) and are distinct from the Afghan refugees who arrived post 1979. As a kid, I remember playing in the village, and inadvertently ''walking'' over a unsuspecting hill and all of sudden being in Afghanistan, only to hear my mom call me back. It was just as trivial then as it is now.
The government of both countries, need to realize this and work to facilatate trade and commerce which will prove beneficial to both impoverished countries and for the long term prospects of the region as a whole.