If by "they", you mean Capcom then the reasons are basically that they lost interest/staff and pretty much pulled out of the arcades. There is so much more money in crap like Resident Evil, Devil May Cry, etc.
But...the upcoming Sengoku Basara X is 2D, a fighter, and from Capcom (Japan even). It might not suck.
If by "they" you mean anyone in particular there are still 2D games being made all the time, even some that aren't on DS. Even some fighters. Arcana Heart, Hokuto no Ken, Melty Blood, KOF XII was just announced a couple of weeks ago.
I just finished Mother 3 last week. f*cking great, that.
Also: Contra for DS. That should be fantastic.