I, too, have only played the Wii version. At the time I couldn't really fathom how the game would be playable with a stick, regardless of the finicky input recognition. Having played W101 since, and mostly reverting to the stick to draw, I can see it being more feasible. With Okami, however, there are a number of "QTE" type scenes that require a series of extremely specific and quick inputs that almost broke the game on Wii. I seriously have never been as angry at a game as I was when redoing one of these scenes for the 20th time. I have no clue how that got past testing. As conjectured above, they probably didn't do enough work adapting the drawing system to motion input.
This version or that, though, I thought the game sucked on the fundamentals. Repetitive, boring level design, too long, lame combat. I recall the old Nintendo IGN team being flabbergasted that Okami won GOTY over Twilight Princess, when Twilight Princess was a much better Zelda-clone than the Zelda-clone that won.