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Agree about the warps. They could have been done better. It's not a terrible system, but it was annoying having to spend a few minutes getting to a warp and it was tricky to remember which was which.
I don't really have any major complaints about the game. I thought it was awesome. The controls were much tighter than they were in PH and allowed for some pretty neat puzzles. GOAT music and mini-games for a handheld Zelda. Solid dungeons and sidequests too. Overall, a very underrated Zelda. Probably my favorite handheld entry after LA.
How about the most obvious improvement: The ability to use the d-pad instead of the stylus in order to move?
Pretty much this. I remember when I first tried Phantom Hourglass the stylus only movement was a big turn off and I ended up not playing the game anymore. Several years later a friend pointd me to a dpad patch that he helped setup on my 3DS and man was it amazing. Other then the lame ocean palace repeat junk and treasure fishing with the stupid crank arm Phantom Hourglass was superb. I went into Spirit tracks on a very big high, with the its own dpad patch and was loving it until I got to the flute thing... and that ended it for me T_T.
Ill give it another shot please tell me the flute thing is a one and done sort of deal pleeeeeeeeease.