Shouldn't 'Numbuh 1' be the leader of KND?

No, operatives' numbers aren't given sequentially. (Of course, everybody in Sector V just happening to be assigned numbers 1 thru 5 is highly implausible, and can probably be chalked up to the KND's backstory changing since the first episode was written.)

Supermodels...spoiled stupid little stick figures mit poofy lips who sink only about zemselves.

After the film he sure as heck should have been, though he was given the choice in Operation I.T and he didn't want it, course he did support Rachel as leader. I would have liked an episode that he was left in charge while she was away, it would have been cool to see if he could handle it.

2012, bring it on!

The Delightful Children once were KND members until they were turned the way the were. Their numbers were .1-.5 so yeah.... Also there was literally an episode where number two's little brother was becoming an operative and he was just told to pick his number so it doesn't go by who was there first or who was best

KND identification numbers are reassigned once their previous holder is decomissioned, resigns or defects. So Numbuh 1 was assigned this number not because he was the first to join or because he's the most important, but because the former Numbuh 1 left the KND. Presumably, he is one of the newest members. That explains how he was invited to the KND by Numbuh 5 and trained by Numbuh 274 at the Antarctic Academy.

The show focuses mainly in Sector V, of which he is the leader. But there are more important members of the KND such as Supreme Leader Numbuh 362.