Websites that force the pop up reminder to add a link to their page onto my home screen. Every. Time. I. Go. To. The. Site. Enough!! I DON’T WANT YOU ON MY HOME SCREEN.
Websites with apps. No, I don’t want to use an Engadget app, nor a NY Times app, nor a Delta Airlines app. I have an app. It’s called Safari. Make your websites work awesome with Safari and you won’t need to waste time and resources building your apps. (I get that notifications from apps can be useful, but those could be handled in other ways, through websites).
Websites that just don’t work right on Safari. And it’s not just sites that use Flash. It’s lazy devs and/or poor QA. And seriously, you don’t test your site thoroughly on iOS? SERIOUSLY???
What do you hate on the iPad?
The iPad Alone 
A) Sites that don’t allow you zoom in on text.
B) Sites that redirect you to Clash of Clans in the App Store (seriously, I’ll never buy an app that I’ve been force-redirected to. Ever!).
Love these! I would also add:
-sites that only allow fixed zoom/text sizes
-sites whose text size doesn’t expand when you switch from portrait to landscape on iPhone (macrumors.com is GREAT about this; others like gizmodo just cram more tiny text across the rows)
-sites like Engadget wherein you can only zoom to one larger text size, which forces a giant, non-removable banner onto the bottom of the page