One for the Morning Glory - John Barnes. Top of my list. Action, adventure, a prince who has lost half of his body, and Highly Unpleasant Things It Is Sometimes Useful To Know.
The Face in the Frost - John Bellairs. Up there with A Wizard of Earthsea for good takes on wizards, and less likely to be found in the course of everyday life.
Speaking of Ursula LeGuin, the first three Earthsea books are a good plan, and I highly recommend Very Far Away from Anywhere Else.
The Phantom Tollbooth - Norton Juster, if she hasn't read it yet, and if the illustrations work correctly on the Kindle.
Has she read The Westing Game - Ellen Raskin? That one's probably in her school library.
Oh, and of course for introductions to SF for someone who likes mysteries, try The Caves of Steel - Asimov.
Second "One for the Morning Glory" - it's brilliant on so many levels.
(Though I'm not totally sure it's age-appropriate. On the other hand if she can read OftMG, you can certainly start her on Pratchett too.)
I bought my niece a Kindle that just arrived and I'm about to load it up with books to give it to her tomorrow for her birthday. I've decided to be a sneaky uncle and include good books that can teach better abilities to think or at least to consider science cool and interesting. She is currently in the 4th Grade with 5th coming after the Summer.
She reads basically at her own grade level so while I'm open to stuffing the Kindle with books to be read when she's ready, I'd like to focus on giving her books she can read now. Ender's Game will be on there most likely. Game of Thrones will not.
What books would you give a youngling? Her interests currently trend toward the young mystery section, Hardy Boys and the like, but in my experience she is very open to trying new books with particular interest in YA fantasy but not much interest in Sci Fi (if I'm doing any other optimizing this year, I'll try to change her opinion on Sci Fi).