You have to admit in such a lopsided tournament, one of India or Pakistan was always going to be screwed. Pakistan lost to India in the group stage and from then on, Pakistan couldn't simply be an equal, they had to be by far the best side in the 4 in order to get to the final.
It's clear they only have this two group structure because they can't find 8 half decent teams for a knockout tournament. The thing is that it's just not worth fussing over. There's more truth of skill a proper ODI series and more prestige in a proper world tournament. The result of the Champions Trophy will override this one in people's minds.