It's not like Dany really HAD a story in S2. She just wanders around Qarth not accomplishing much of anything.
Wouldn't work for TV. Neither would her visions in the House of the Undying.
I felt the Qarth chapters in teh book were a bit aimless myself, with the exception of the House of the Undying. She shows up in the city, asks for help, doesn't get any, oh look someone sent a boat.
I'm not surprised they changed it around for TV so that something more actually happens, although I do wish they'd been more ambitious with the House scenes.