Rahul is an opener, and one spot is already sealed (Rohit). In addition, India wasted too much time with Rahane and Dhawan even though Rahul is better. To take matters into perspective, Dhawan is considered mediocre in India but with with the same stats, he would already be an ODI great for Pakistan and the second best opener after Saeed Anwar. That alone sums up the gulf between the two teams when it comes to batting.
Secondly, it's not as if Babar has been winning matches for Pakistan on his own but has been let down by his teammates. He scored a lot of runs in Australia but his accumulation was taking the team nowhere. At the moment, he doesn't have a power game and lacks impact, something that Rahul has in his armory, which makes him a superior all-round batsman.
If Babar does not improve his power game, he will not win many ODIs for Pakistan in spite of having ATG level stats. He will end up like Amla or Williamson, which is why it is imperative that he must work on his ability to play big shots.