I agree that Minish Cap is a really good game that I don't regret having paid attention to. I didn't really know that it was under the radar, though until I took a peek at the sales numbers and saw that they are comparatively small when put against the big sellers like Ocarina of Time and Twilight Princess:
http://gamrreview.vgchartz.com/sales-data/4572/the-legend-of-zelda-the-minish-cap/
I think it's better than the DS games and my favorite portable Zelda, which isn't really saying much since these three are also the only ones I've played. While the game was a bit on the short side, the kinstone fusions and other side-quests gave it a lot of side stuff to do and see.
I also find some of the situations in the game enjoyable because of how they are, like the part where you have to get back the books to get to elder Librari. I never thought doing a book collecting errand would be so important along with the unique situation of having to help a minish drop one of the books off the cieling and escaping cats, talking to animals and the like. I guess it's a little bit of that creativity that I think sets Minish Cap from most other games in the series. The fact that the developers made it so even the most mundane things for normal-sized Link become a grand adventure in the series' tradition when you turn into minish size gave a really interesting spin to Zelda's usual adventure element, in my opinion.