If Rohit and Kohli are getting out early in the innings, it means the conditions are not batting friendly and that it needs grafting to get to a good defendable score. Shankar did something like that in NZ where he and Ambati Rayudu pulled India out of a rut and took them to a score where Hardik came out and unleashed his strokes. And we won that game.
Where I would worry about Shankar is when India have set a good platform to launch big towards the end and we have only a few balls left and Shankar has to come out and start blazing from the word go. Which is what happened in the last game and he showed that he does not yet have the game for it. He is more of a classical batsman who takes time to get going and plays mostly proper cricketing shots and is conventional in every sense. So it would then be a case of selecting for the conditions - if its seaming, Shankar plays as his bowling becomes useful. If it's not seaming and is a bright sunny day, Karthik plays as he has the game to come out and start blazing. I would play Pant only in case of an injury to one of the batsmen.