I don't want your iPad-optimized web site
One is the tendency to auto-convert themselves into app-like interfaces. Google+, for all its attempts to catch Facebook, does this and it makes me hate their service (e.g. create a Page on my desktop and love it, go to my iPad and find 90% of the Page's capabilities are simply missing). Since I know the device can handle a normal web page, I am just angry when a site effectively hides itself from me.
A related "feature" is this assumption that there must be something wrong with me for using the web page: sites constantly popping up reminders that they have apps. If I wanted the app I would have installed it.
The second problem is sites adding arbitrary restrictions. Pinch-to-zoom is awesome until some bone-headed web site decides all by itself that its layout will actively fight this. Less available screen space, broken scrolling, the list goes on. You know what, I know what size I want my font to be, not you.
So please, web sites, fire your iPad "optimizers" and let your sites shine for what they are. Very few web sites are truly similar to apps, so stop making them that way.