An interview conducted by Japanese magazine Famitsu, Nintendo's Hideki Konno, producer of Nintendogs + cats and head of the Nintendo 3DS project, reveals that when he first joined the project for the DS successor, 3D was not part of the initial plan.
Konno goes on to state that while the project to design the successor to the DS began once the DS was completed, it wasn't until after 2008 that they considered using 3D in games once again. The initial target for a DS successor was to make a new system backwards compatible. This meant having two screens and the bottom screen being a touch panel.
Early tests of 3D involved connecting a Wii running Mario Kart to a 3D LCD panel, which received positive feedback. Other demo's consisted of 3D figures of Mario and Luigi, which also impressed viewers.
Another 3DS feature, the gyro, was not added until after the specs were finalised by Nintendo. The gyro itself wasn't decided upon until before last year's E3.