The 3D screen, while being a fun gimmick, is expensive to produce. At the same time it imposes a heavy hit to battery life due to both the energy costs of running the parallax barrier and the energy costs of the more powerful backlight needed to send enough light through that barrier. That's a big reason the original 3DS, despite its relatively puny SoC, only gets 3-5 hours on a single charge (typically closer to the former). So producing a model without the 3D screen, along with solving their unsafe-for-children problem, scratches an itch in the market for a version of the console without the 3D screen and its drawbacks.
The issue however is as you note: the rest of the design. I for one was hoping for a 3DS sans the 3D screen and that's it; maintain the size and the clamshell, just ditch the 3D screen. Instead we have something that looks like the bastard son of a tablet and a 3DS. Given the market Nintendo is going for (the under 7 crowd) this may make all the sense in the world for as far as I know; Nintendo does do their research before going ahead with their spacier ideas. But I'll freely admit it's not the 2DS I was wanting.