I've never tried the Dead or Alive games, so it's SSFIV for me. I might pick up DoA at a later date, though..
My only gripe is the control scheme; I use a Tournament edition Fightstick on the 360 version, which is essentially a necessity if you want to really handle your executions well.
Chances are, I'll still play the 3DS version on a regular basis purely for the portable factor. Aside from the controls and slight graphical changes, both games are identical (if anything, the 3DS has slightly more content).