It wasn't always like that. When Pakistan started out, they were lucky to have Fazal Mahmood, the subcontinent's first worldclass pacer, but after he left, Pakistan relied mainly on their batting/spin until the mid-70s when Imran Khan came to the scene. Since then Pakistan's bowling has been consistently better than India with few exceptions. Pakistan and India both have produced worldclass spinners but when unless you have a Warne or Murali then pace matters more, especially outside the subcontinent.
Imran was an exceptional case, as the training and conditions in Pakistan taught him to be a medium pacer, and it was only through bowling in English counties, remodeling his action and aspiring to be like other great pacers that he transformed himself. He could easily have been one of innumerable subcontinent trundlers had he stuck to the same system.
Why does Pakistan continue to produce better pacers? I think it's a combination of a few reasons. Diet perhaps, and the fact that Pakistanis tend to play tape-ball cricket which helps in pace bowling more than a normal tennis ball. More than this, we are inspired by our biggest national heroes, so young Indians growing up would want to emulate Gavaskar and Tendulkar while Pakistanis growing up want to bowl pace like Imran, Wasim, Waqar and Shoaib. Indians of late look up to Wasim/Waqar as their role models, and the last few years we have seen better quality Indian pace bowling than ever in the 90s, Srinath aside.
