Now anyone who's read my posts knows that I'm an X-Box fan ... However, I have to say, I thought the X-Box controller was awkward at first. But I got used to it after playing for only a short time. It was the same kindof thing with the Dreamcast controller, and even the PS2 controller. (I never owned a PS1, so going from Dreamcast -> PS2 was a change for me).
I agree with the button placement being sortof awkward at first, although with NHL 2002 I do not have any problems what-so-ever with pressing the correct button. I do have problems with accidently pressing the wrong button in Halo occasionally, but I think thats more because I hardly ever push the face buttons (you mostly just use the L and R triggers, at least for me, because I have L set to Jump).
In any case, just like your console choice, controllers come down to preference. If you love the X-Box and want a better controller though, I recommend the Pelican one. The Madcatz controller has nice button placement but I found myself struggling to get my thumb to reach the right analog stick and still be able to have my index finger on the right trigger ... Not a good thing for Halo Deathmatch!!
The Pelican controller is very very similar to the Dreamcast one. It is about the same size. The only problems I've had with the Pelican controller is that the D-Pad doesn't feel as nice as the Microsoft one (Being a user of the Microsoft Sidewinder for ages now, I am very used to the MS D-Pad with no cross on it), and the triggers are not as high quality as the Microsoft ones (although all of the 3rd party controllers I've tried so far have this same feel to it).
I'll definitely have to give the Japanese controller a try if/when it gets released in North America, although I think the D-Pad looks kindof nasty! I also liked how the original X-Box controller had different "feels" for each of the analog pads, which the Japanese one doesn't seem to have.