Well obviously to make money.
However, like you mentioned, it's going to create a stack of games that a large majority of 3DS owners will not be able to play and I really doubt a lot of people are going to update their 3DS either.
If I were to guess, I'd say that no game with "3DS" on the package would be unplayable with an older 3DS. Just like with the Wii and Wii U, they'll just have different controller options. You could play Xenoblade Chronicles with a Wiimote and Nunchuk, for example. Of course, you SHOULD have played it with the Classic Controller attachment, but you had the option of playing it with the out-of-box set-up.
Same here. People with the newer systems will have the advantage because a C-stick is awesome but people with the older systems will still have a controller option that will make the games functional... if not exactly ideal.
But that's just a guess.