I can understand people's initial objections to the 3DS not having a second stick but I really don't understand why so many people thought Nintendo were going to divide the 3DS user-base at this stage, effectively alienating the 15+ million people who bought their system first.
Give people a second stick and while you might placate a relatively small number of people who can't live without dual analogue, you are likely to give a much greater number of people the impression that buying the 3DS is a risk because Nintendo could at any moment introduce a new version which renders the old obsolete. (Same goes for upping the resolution)