I finished the game today. As far as Zelda games go, it's easily not my favorite one. That said, it had a lot of high points.
The control with the stylus worked well enough for normal stuff (once you got used to it), but all the extra control you have over the items was great. The same goes for making notes on the maps, but it got annoying that every time someone gave you a clue or a hint they told you to write it down. It was nice the first couple of times before I got used to having it, afterwards it was just like the game didn't expect me to grow.
A lot of the dungeons were to easy, and I remember that being a problem with the Wind Waker. There's at least some justification here as a portable game with long drawn out dungeons wouldn't work out so well for quick gaming sessions. You could tell that was what they had in mind because all the dungeons had shortcuts that you'd open up along the way so if you had to stop playing you wouldn't lose much progress. The repeating dungeon also got to be a pain, but in the end I think it was my favorite one of the bunch because it just had the most interesting stuff.
Finally, I'm still not a fan of boating around to get to places. It feels like it breaks the game up instead of making it bigger, mostly because each place is so small. Again, I suspect it was somewhat deliberate to make the game more portable, so I don't know if I really want to fault it that much here.
So yeah, it was fun and all that, but I'm sorta glad the game is done. What it did do was make me want to try to get into the Twilight Princess again and go at a real Zelda game. It seems all the portable Zelda all make me feel like that, although I never played those season ones that came out on the Game Boy Color. Something about them just feels a little off.