I can understand the D pad thing. I've never had a problem myself, but they are getting smaller on Nintendo systems, so I could see why people do.
But the B button feeling like it's broken? Maybe your B button is broken, as it feels like the rest to me. I love the oddly shapen buttons. It helps me remember controls quicker. I never had a huge problem learning controls on other systems or anything, but it is still quicker. I love the triggers too, they feel perfect. The shape of it is great, it really does just melt into your hands (corny, but I'm just trying to get across how comfortable it is). The Z button's stupid.
I think the GC pads main problem is that it's differences with more popular systems. So obviously games are going to be designed round a Dual Shock rather than a GC pad, and suffer when ported. If the PS2 had a GC like pad, I think a lot of problems would disappear.
Now if you want a controller which feels like a cheap piece of crap, look no further than the DC's. Even that was perfectly managable though.