There are many difficulties regarding a federation . First is that place is so backward it will take us forever to bring them to our level . If $ 100 billion dollar from America couldn't improve anything what makes you think we can? they are corrupt to the core and keep on fighting with each other .
This is a great question. One that needs to be figured out -- I for one do not have an answer.
Possible sketch of an answer:
What can be done is to have a loose federation where for the first 10-20 years -- even movement is restricted between the two confederating states -- we go back to 2010 or say 2005 no visas needed but you need to apply for a domicile for long term stay. To make sure these go to the most needy people you can hold an auction so businessmen, traders, educated people get them. You can also have quotas for poorer people.
Afghans are given preference in titular leadership positions -- for example the titular federation President will always be an Afghan for the first 10-20 years and then only from a minority for the next 10-20 say Sindhi, Baloch, Tajik, etc.
The Durand line will remain some sort of a barrier between Afghans and Pakistanis having to apply for moving across (see proposed auction based and quota based domicile system). Other stuff:
1.
Free flow of commerce
2.
1 common currency (say the: New Dirham) -- the Afghani and Rupee would continue and be allowed to be used in local transactions (Afghani in Pakistan and Rupee in Afghanistan) to be phased out in favor of the "New Dirham" in 10-20 years
3.
A joint High Command: You keep separate ANSF and PakMil structures ... just have a top level command based on say NATO but start formation of diverse elite units [for some military mind to answer this - I would not know the first thing here] But think in NATO you have relatively backward units like say Iceland(?) and on the other hand you have the UK, USA, etc.
4. A single foreign policy
5.
A confederation upper house (you still have the Afghan and Pakistani upper and lower houses)
6. You have a titular president (Afghan for 1st 20 years) then elected like current Pakistani President
7. Still have separate executive structures Pakistani Prime Minister and Afghan President (or Prime Minister)
8.
National Languages: take the example of India. Persian, Urdu, Pashto, Punjabi, Balochi, would recognized as heritage languages. Persian would be the eventual national language (like Hebrew in Israel) with English continuing to be official language and Arabic can be elevated to some sort of ceremonial language.
9.
Extension of special neighbor status of the CARs and China, India and Iran (primarily trade)
What makes you think 200 million Pakistani's will be okay with the name Afghanistan ?
Well that is the key question -- if Pakistanis cannot form a confederation based on the objection to a name then they simply don't want/deserve one. I should think both Afghans and Pakistanis should be OK for example if the world says you can have your confederation but you will call it Poultry-farmistan -- substance over style.
This is a similar argument to what Afghans cite as their 5000 year history vs Pakistan 70 year history. The content matters not the cover is what I should think.
This is a 100 year project -- maybe folks might want it -- maybe not.