The root cause is the ideological divide between the Sunnis and Shias. Arab states especially Saudi Arabia and GCC states have been funding extremist Deobandi Sunnis and Wahabis in Pakistan, since the Aghan Jihad, whereas Iran has been funding Shia militant groups such as the Sipah-e-Muhammad Pakistan, resulting in tit for tat attacks on each other.
The reality is that Pakistan has became a battleground between Saudi Arabia funded Deobandi Sunni and Wahabis and Iran funded Shias causing deaths of thousands of innocent Muslims. Amongst the culprits blamed for the killing are Al-Qaeda working with local sectarian groups to kill what they perceive as 'Shia apostates'.
Will the situation improve? Not likely unless and until there is a change of mindsets, and that is near impossible. Ideological differences will always remain.
