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There's just something about the Wiimote and this game that don't click for me. Maybe I need to play it a bit more, but it just seems really frustrating to draw on the ink accurately. Also, the battle system seems a bit odd due to the wagging.
I'm only about an hour or so in the game, so does this get better? Did you have this issue and then get used to it? Should I just trade it in for a PS2 version so I can use the analog stick?
You'll get used to it. While the PS2 version is the most stable, there are some things about it that'll drive you insane that the Wii version fixed. On the PS2 version, the cutscenes are unskippable, and the brush feels really slow with an analog stick. Once you adjust to the Wiimote for drawing, you'll never be able to go back.
Feel free to request an online match anytime. Check my profile to see my Wii Number and Friend Codes.