Tons of films that became beloved failed in their original theatrical run. Hopefully someone more knowledgable with Hindi films will help me out here 'cause the only Hindi film I can think of is Silsila, but I know Citizen Kane, It's a Wonderful Life, and the Wizard of Oz were flops and the list goes on and on but hopefully you get the point. The audience has to find the film for it to be successful. And having the "right" family and the right connections definitely helps present the actor and the film to the audience. Some of Shahid's flops might have not been if they had had a more influential actor even if the finished product wasn't as good.
Two more thoughts, everyone assumes that the films which Shahid turned down would have done just as well if he had done them which is not necessarily true. Lots of times he is only rumored to have turned them down so it might not even be true they were ever offered. He has said many times in many ways he can only choose from what he is offered. He can always choose to do nothing but that is a risk that hasn't paid off in the past.
Second, I am not going to go into great detail but it really does seem like SK has had dreadful luck in addition to definite lack of support from Bollywood if not worse. For example I firmly believe Kaminey would have been a clean hit if Mexican bird flu had not closed cinemas and delayed the opening. I remember that time and even when cinemas opened people were nervous about catching it and stayed away from crowded places.
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