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This is great point which you mentioned about Afghanistan cricket team lineup. Their team relies on few key batters which means they win big or lose big. Having too many all rounders as you mentioned can be problem because they are not as good at batting or bowling as specialists which makes team less consistent. In contrast Pakistan with more dedicated batsmen has more stable and reliable foundation. Your analysis is good for Afghanistan to become top team they will need to find better balance in their squad and rely less on all rounders.
You are right, the number of all-rounders in Afghanistan's squad was four, whereas the maximum number of all-rounders was supposed to be two, but there were four. In this case, adding a batsman and a bowler would have made Afghanistan's squad much stronger. Rashid Khan and Mohammad Nabi are two experienced players, so these two should be kept in the squad for now and Noor Ahmed should be included in the squad as a bowler. It is not reasonable to have four all-rounders for now.