I have looked into the options in my PA28-181 and I also think that mounting it to the yoke hides instruments or switches you really want to be able to see. I dont personally want to mount it onto any of the windows either because it blocks out a large area from which an aircraft might be coming.
For me, I just use it on my lap. I use a panel mounted GPS as my main unit. I do however put the iPAd away for take off's and landing, otherwise you end up with a small collection of charts, kneeboard and iPad on your lap, and you cant move the yoke fully.
I also concur with the touching the screen problem. If you take SkyDemon for example, you might want to touch the screen to get airfield info, or adjust a route in the air, but I wish there was a button to 'lock' the screen when you dont want to make an input. A few times I have inadvertently moved the track or the plane symbol or something. I'm sure I have seen apps that do allow the iPad to disable screen input - though I cant recall what app that might have been.