A lot of countries in the world are geographically fragmented, but they are thriving without any problem. Most important point is, common people and leadership in both wings in 1947 accepted that kind of Pakistan wholeheartedly knowing the divided geography. Agitation in East Pakistan was nothing to do with geography. Even if East and West Pakistan was contiguous and Pakistani leadership maintained same policy, still agitation for autonomy and eventual independence would have arisen surely.
Main thing was marginalization of Bengalis in Pakistani state structure. As West Pakistan inherited the big army and bureaucracy, it's people started to think themselves as more than equal. 'Martial' 'bastion of power' 'real Pakistani', 'real Muslim' these narrative permeated to a large section of West Pakistani populace and they started to see the inhabitants of East Pakistan as a subject to rule , lesser Pakistani and lesser Muslim who need conversion. They started to think West Pakistan as the real Pakistan, a 'bastion of power' and East Pakistan as an extra, meant to serve the interest of real Pakistan aka West Pakistan, even be used as a bargaining chip in their showdown with India. These line of thinking made them unapologetic and careless about the perverse exploitative and discriminative system on places and hardened them to accept any compromise or fair sharing. These line of thinking was the main reason why West Pakistan based powerful military-bureaucracy nexus from the beginning started to undermine the democratic course of the new country. Because accepting democracy means accepting Bengalis as equal, which they were not willing to entertain. Palace coup, military coup became the norm, only goal was to deny the rightful share of Bengalis and make them a marginalized, colonial subject serving the interest of West Pakistan.