GameSetWatch has a nice essay up from Gregory Weir, who takes a look at why Puzzle Quest was so damn successful at creating a satisfying hybrid.
Weir takes a reasonably detailed look at how designers successfully married RPG and match 3 elements, and why Puzzle Quest is the best example of a well deployed hybrid design. He offers the following words for designers:
When creating genre-spanning games, developers should follow Puzzle Quest's example. They should choose genres that can interact well with each other, and look at places where the tropes of one genre can be exploited, as with Puzzle Quest's use of puzzle gameplay as a battle system.
Additionally, developers should not fall into the trap of believing that the novelty of genre fusion will make players forgive a shoddy implementation of the individual genres. An FPS/RPG hybrid need not be the best FPS or the best RPG, but it should present each genre in a way that it could at least hold its own against single-genre games. Combining shoddy implementations of two genres does not lead to a single good game, but a sort of shambling Frankenstein's monster. Puzzle Quest, on the other hand, is a true hybrid, taking two well-executed genre games and combining them into an even better whole.
Anyways, nice quick read on a nice game — Weir has some interesting points on the implementation of various design elements.