All teams and players have their nemesis somewhere, same applies to batting units. Indians have generally struggled against conventional swing, SENAW against spin, Bangladesh against seam, Australia also against swing, England against reverse swing etc.
But Pakistan is an unusual team because right throughout its history bounce+pace has been an Achilles heel, even for great Pakistani batsmen like Zaheer Abbas, Miandad, Younis etc. That is a main reason why PCT couldn't conquer Australia and South Africa when they had brilliant bowling units to get the hosts out cheaply twice. Overall they have been excellent against spin, ok against seam, good against swing in fact easily best apart from England/South Africa (mainly 2004-12) and comfortably ahead of India even in recent times.
We saw in the recently concluded South Africa tour where the batsmen were relatively at ease against exaggerated lateral movement pitched up. But when the SA bowlers pitched it halfway down the pitch (as low as 135+, forget express pace like Akhtar, Lee) even the well set batsmen started gifting wickets. To make matters worse most of the wicket taking deliveries weren't well directed bouncers, I am sure many Australian and Indian batsmen would have been ruthless in punishment of those kind of half trackers. Duanne Olivier made his name just by exploiting this weakness which wasn't limited to 1 or 2 batsmen but almost the entire unit, he didn't have other major tools at his disposal. The Lankans were at ease against him in the next series. Today again we saw a surrender against the rising deliveries. These were batsmen in their prime, not 38 year olds with declining reflexes and hand-eye.
My question is why is it the case? The way I understand cricket, simulating swing, seam and spin are harder in net sessions. Simulating steep bounce is very straightforward. You don't even need a proper net session, remember how we used to play gully cricket, when the tennis ball was dipped in water suddenly it would start bouncing steeply. Also there are specifically designed hard plastic balls which can help even low grade gully players learn to tackle bounce. For international teams I am sure they have the best equipment to generate bounce in training sessions. Of all the types of bowling it is my belief that learning to negotiate bounce should be the easiest. Lots of practice and courage are the key ingredients. Technique isn't tested that much unlike against spin, seam or swing, many high quality batsmen who initially struggled against bounce found a way around it without a big change in technique like Steve Waugh, Ganguly, Chanderpaul, Sehwag. Also with bouncers many modes of dismissals are eliminated: bowled, LBW, stumping completely and caught behinds (and straight of the wicket) are rarer.
Indian batsmen were vulnerable against this kind of bowling till 60s/70s, but gradually improved despite shortage of Garners, Holdings, Ambroses and Morkels in our setup or WACA/Gabba/Wanderers kind of domestic pitches. We couldn't improve much against swing because of lack of quality swing bowlers in our domestics. We have deteriorated against spin of late because more of our pitches in FC are too much in favor of seamers resulting in shortage of high quality domestic spinners. Batting against seam has improved for the reason mentioned above. This suggests that handling bounce can be easily set right in the nets under purview of the coach.
The possible conclusions are that-
1) Pak cricket system hasn't identified the problem or considers this a small/non-factor.
2) There is something wrong in the way Pakistani batsmen are groomed in nets, maybe a fault in the training methodology right from junior cricket.
3) Pakistani bowlers (including the ATGs) don't use bouncers as much as other teams, relying more on LBWs and bowleds. Maybe this is an issue stemming from domestics played on low bouncing pitches. If bowlers don't use this weapon, batsmen too aren't sufficiently trained or made aware of their deficit. By the time they make it to internationals and play in SENA it is too late and then begins the mental hurdle. That makes way for my 4th point.
4) After being shielded from pace+bounce at a lower level, when the transition to internationals is made, post first encounter with this kind of bowling the battle becomes mental. There is a culture of fear for the batsmen against short pitched bowling, they are afraid of getting hit, so mental conditioning should be better to solve the problem.
For Indians, Gavaskar, Vishwanath and Amarnath led the way forward and forced a change in batting psychology. If you read about our cricket history before that a common recurring theme is Indian batsmen being afraid of the quicks and backing away towards the legside. This can be logically explained because our 60s/70s batsmen were shielded from physical injury in Ranji/Duleep and when they made their debuts the jarring experience with tall pacy quicks had a lifelong impression. Swing, seam can dismiss a batsman, make him look like a fool but with short pitched stuff there is a fear of getting badly injured.
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