I have little doubt that there won't even be an Iron Throne at the end of the books.I expect Aegon to conquer King's Landing and have the support of the people, and be considered a great King...for a brief period of time. Then the Greyscale plague starts, and wipes out half of the population. Then Daenerys shows up and doesn't know what to do, and decides she wants the throne for herself (not bend the knee to her nephew), and then everyone ends up hating both.
It works for 2 reasons:
1) The 'perfect king' is undone by things outside his control.
2) The entitled queen is undone by her lust for power at the expense of earning it (like most of her story).
I don't think the show will go down like that, obviously (they probably want a fairy-tale ending), but I have little doubt that in the books Daenerys will not sit on the Iron Throne at the end.