Giving more buttons to developers means they will take advantage of it and make stuff that wouldn't work on the old 3DS. It won't phase out the 3DS right away, but I'd not expect to see many titles for the old 3DS in 2 years. You're right if you want to call it a stopgap, in that respect.
A really important feature is the control scheme. While the new 3DS isn't as powerful as a Vita/360/PS3/etc., having parity in the number of buttons means that games that aren't hardware intensive can release on more systems, including the new 3DS without requiring developers to make a specific addition (onto the touch screen, let's say) to make the game work on only 1 control stick and 2 shoulder buttons. Having 4 shoulder buttons, 2 sticks, and 4 face buttons means that it's easier for indie developers to release on the new 3DS.