It's a mistake on iPad games to place the virtual controls on the bottom corners of the screen. The optimal place to hold an iPad is gripping the middle of each side. The controls should be easily accessible from that middle location. Holding it from the bottom is completely unnatural, unbalanced and causes your hands to get quickly fatigued. All handheld gaming systems are designed to be held on the middle of the device (PS Vita is good example). Hopefully developers will start thinking about better ergonomics when designing new iPad compatible game.
You have a point, but it never bothered me personally. I rest each bottom corner of the ipad on the cup of the palms and they basically carry the majority of the ipad's weight there. I use the middle and ring finger to support the back, while the pointer fingers can either help support the back, or i can use them as a means to touch higher in the screen.
Horizon Chase is the game that finally pushed me over the top. Like everyone I love playing it. However I can only play so long before my wrist get tired which causes me to start moving my grip up and then accidentally hit the wrong controls. Woe is me! I think more people unknowing have issues. I often hear people say they prefer using an iPhone over the iPad for playing games. I think this might be one of the reasons.