The Legend of Zelda: Phantom Hourglass
I've been pouring myself into Phantom Hourglass at every available opportunity. I really, really like this game. It's damn fun to play - the dungeons are pure genius. Sprinkle in island puzzles - in the form of cartography challenges and treasure hunts - and it's just awesome. The story isn't as compelling as Wind Waker's or Twilight Princess's, but moreso than Minish Cap's; for a handheld-sized presentation, it's really remarkable. But I still, still don't like the controls.
Navigating the ship is something I thought would turn out very poorly, but it's actually one of the cooler features of the game. When you're at sea, you bring up your sea chart and plot out your course using the stylus. More often than not, you'll simply draw a line (avoiding obstacles in the way) between yourself and your destination. Sometimes you'll need to bring up the chart again and readjust, such as to evade or chase another vessel, but fortunately this juggling act doesn't come up very often.
The first upgrade your ship gets is a cannon, which operates similarly to Wind Waker's, except that it doesn't use your bombs; the cannon's ammo is infinite. Once you get it you'll start running into enemies at sea that need to be blasted to kingdom come, and firing on them is a simple matter of tapping them on the screen.
The second ship upgrade is the grabber arm, which you use like Wind Waker's maritime clawshot to retrieve sunken treasure. The difference here is that the grabber has HP, and bringing up chests invokes a minigame that requires you to avoid mines. Repairing the grabber arm costs rupees, and you can only repair it at the main port, so there's a strong motivation to take it slow and avoid mines rather than try to barrel through the minigame.
Lastly, you can get a fishing rod. Yes, fishing! Chase a fish shadow on the sea chart, and use the rod to engage the fishing minigame. It's a simple gesture-oriented affair, and in the end, you get... well, a fish.
On top of all the deep-sea activities, there is a ton of stuff to do in the world of Phantom Hourglass. It strongly embraces the Zelda philosophy of a litany of background quests, while at the same time making it surprisingly easy to skip it all and move right on to the next part of the main quest.
Something that's been bugging me throughout is that there are no heart pieces. Bosses give up full heart containers, and I actually just bought another full container off a ship merchant (the only one I've seen so far), but in general my HP is being capped at a relatively low level. This has the net effect of making the game more challenging than most Zeldas, as the amount of enemies you encounter and the damage they deal actually scale proportionally with the amount of health you have.
Progress: Looking for more Sea Charts