I don't really have any issue with Dany's story as it is. I just hate how disconnected it is. It makes it one of the most boring, for me. Almost every single character in Westeros is part of a great narrative network. Even more isolated characters like Bran and Rickon. They meet people, see things, and have an impact on the world around them. And there's always that anticipation of what will happen when they do meet people elsewhere. Jon and Bran might be separate, but they're brothers, on the same continent, floating around the same area. There's a shred of hope they'll meet, even if they don't. And then when major events happen to another character, it always has a lasting impact on the narrative of another. What happens to Robb impacts Tywin, which impacts everyone at King's Landing. Tyrion is at King's Landing, and thus impacts Sansa. Sansa is friendly with the Tyrells, and so what happens to her impacts them, along with Shae.
Dany, on the other hand, has been isolated for three seasons. With the exception of Barristan Selmy's arrival, and the assassination plot in season one, everything that happens to her could be shot and cut and filmed separately as an entirely different show. You really wouldn't notice the difference. She's out of the loop that is the Westeros narrative arc.
And that is the point. Her story is more personal, of development, with the promise she will bring the shit down in Westeros. And she has been mentioned in Westeros by the likes of Varys. But after three seasons it really is more of the same shit with no actual impact on any other narrative arc.
It's like, you've got:
North vs. Lannister War / Joffrey insanity / Tyrion + Sansa + Shae / Arya + The Hound / Brotherhood without Banners / Stannis + Red Priestess / Tyrells / Jon + Wildlings + Watch / Bran + Hodor + co / White Walkers / etc
Several distinct plot threads all woven together in a great narrative tapestry.
Then you've got:
Dany + Dragons / Slaves
It's like a show within a show. A fun one, but totally devoid of the awesome politics and back-and-forthing of shit going in Westeros.