The Wii and its controller may have been the big talk of E3, but recent comments by Nintendo's Shigeru Miyamoto suggest that what we saw at the show was not the final thing. Speaking with Japan's Famitsu, the Nintendo spokesperson and father of Mario and Zelda said, "We're still debating on the area of how many buttons to use."
Miyamoto was responding to a question about difficulties Nintendo had in designing the controller. He attested to having many stories of such difficulties to share, before letting slip the above comment. It's possible that Miyamoto was merely stating that Nintendo's designers still argue about their decision regarding the button count, but the E3 design is final. Alternatively, it's possible that Nintendo is actually considering making some changes to the design before release. We'll have to wait for further clarification (or for the Wii's next showing).