My favorite version is Origins. DoS is as everyone has already stated, ridiculously easy. On the NES and Origins i think the Black Mages misses at least half the time whereas with DoS he's hitting around 90-95% of the time. Both my thief and fighter were getting 2-hits from the start and by level 5 they were doing 3-hits.

The music in DoS is pretty much the same as in Origins, but let flashy in order to get it to run on the GBA hardware. The nice thing about Origins is that you can choose to play Hard Mode, which makes the gameplay closer to the original NES (things are more expensive and your magic level max out at 9).

Graphics-wise Origins and DoS are very similar, though I do think the characters in DoS are a bit squished relative to their Origins counterparts.

That's my take on it. DoS is nice if you are always on the go, but I much prefer Origins.