Acutally, this is not true. Believe it or not, the DC version is still missing animation frames. Yes, it's true. If you look at Vega and T. Hawk, their backwards walking animation is missing in the DC version, but they're present in the Saturn version, just as they should be.
The graphics in the DC version are suffering as well. I have all 3 versions of the game and have compared them side by side. The DC version suffers from the same pixelization problems like MvC2, 3rd Strike, and CvS2. In order to save space on disk, Capcom compressed the sprites to a smaller size, and the DC simply enlarges them before placing them on-screen, giving you the pixelated mess you see on screen. in the Saturn version however, the sprites are uncompressed, and as a result look much sharper and more detailed. (On a side note, SF3: W impact for the DC also has uncompressed sprites, but 3rd Strike's sprites were compressed, which is why so many people think W impact looked much better than 3rd Strike on the DC)
Additionally, if you were to compare the 2 versions side by side, you'd see that the sprites in the DC version are skinnier than in the Saturn version. This has a serious negative impact on gameplay. Since the sprites are thinner, that also means the hit boxes on the sprites are thinner too. What that means is that the properties of the physics in the game are now changed. In short, since the hit boxes are smaller in the DC version, certain combos either do not work on the DC version, or are much more difficult to perform, as you have to be right on top of the other character.
Lastly, the physics of the game itself are out of whack on the DC version. The timing of Custom combos is out of whack on the DC version, something about the way V-ism works on the DC version has different properties than the arcade version. Additionally, Dhalism's streched out limbs don't have the same priority they do in the Arcade and Saturn versions.
Sorry to be such a stickler about it, but I did some serious research on this topic, both on my own and on the net, as SFA3/SFZ3 is quite possibly my favorite game of all-time.
I always thought this was due to the original arcade hardware having a lower screen resolution than the Dreamcast. Since redoing the graphics (scanning, cleaning and colouring) would be insanely expensive they just used them as-is. Also consider the fact that the capacity of a GD-ROM is much greater than a CD-ROM and that the uncompressed size of the MAME SFA3 ROM is a mere 46MB.
EDIT: The "thinner" graphics may be due to the different screen aspect ratios of the CPS2, Saturn and Dreamcast.