It wouldn't change that some pokemon are better than others, but would increase diversity. Pokemon with very good typing, defensive stats and defensive moves are currently excluded of the game just because of their low CP (coming back to cheating: shavers, etc). It's not only CP's fault. It's CP placement together with lack of anti-cheating measures.
To be fair, I don't think Niantic will ever get rid of CP (it's one of their signatures). And in the same way they won't ever be able to stop people from using multiple accounts. Therefore, there is the need for a way of gym sorting other than CP.
I'm looking forward to the "gym rework" to find out whether they are still able to surprise us