They open up pandora's box and allow game devs to focus on superficialities to increase revenue (such as a bonus level, ways to skip level, etc..). Were the playing field completely even -- no in-app purchases -- gameplay would necessarily have to win out and people might spend more time reading mobile game reviews.
When you can be angry bird and get on the top grossing list for a long, long time because you got in-app purchases, I believe it skews the data and as a result, many are poorly informed as to which game truly is the best.