I've read both Hana Kimi and Boku ni Natta Watashi, and I have to say that I enjoyed Boku ni Natta Watashi more. Each has their good points and bad points, but--without taking length into account--I would read Boku ni Natta Watashi again (actually, I have read it more than once), while I wouldn't read Hana Kimi again. I think that, on the whole, the characters in Boku ni Natta Watashi are much more realistic (though, truthfully, neither story line is entirely plausible).
The only thing I can think of that Hana Kimi did better than Boku ni Natta Watashi is that it took longer for the main male lead to discover his roommate was actually female. That drawn out process added drama to it and made the focus more on the gender bending aspect than the romance aspect.
Boku ni Natta Watashi, on the other hand, has a host of things that make it better than Hana Kimi. As I've mentioned, I find the characters more realistic overall. Adding to that, the sexuality aspect is dealt with much more in Boku ni Natta Watashi than it is in Hana Kimi. (Of course one could tie the sexuality aspect in to the gender bending aspect--in that sexuality is often defined by gender.) Either way, a boy and girl living together as teenagers and wanting to have sex seems much more realistic to me.
The ending to Boku ni Natta Watashi seemed much more realistic to me as well. As realistic as a shoujo manga can be, anyway.
Momoko's issues with returning to life as a girl were very interesting. She even slips up and uses a male pronoun to describe herself. I like that Shimaki-san went there and illustrated those issues.
Aside from the story line, I love this manga for the art. I'm very fond of Shimaki Ako's art style and similar art styles.