Hmm...well, I think it's kind of simple. Ninja Gaiden, since it's game on Xbox, is thought of as a big console game. When people think of "Ninja Gaiden" on DS, without even thinking or looking about it, they will perceive it as not as good or worth the time to play. Same with Assassin's Creed DS, Call of Duty 4 DS, etc etc. I think if Ninja Gaiden DS were like, the NES versions of the series on the DS as a retro pack, sales would be much better.
God of War and so forth may get a pass because it's on the PSP and looks like the PS2 game with production values that at least LOOK like they are comparable.
I think it's simply perception. I hear a lot of people talking about looking forward to Ninja Gaiden 2, preordering it and the like. When I point out the Ninja Gaiden DS game and if they're tried it, I get scoffs. Plus, the perception of stylus only controls sucking ass doesn't help.
That's just my thoughts and observations.