Well, the N64 version is generally the same game with slightly worse graphics, one or two less enemy types and some minor changes. The N64 controls feel more natural, but the DCs ABXY scheme gets the job done well enough for me, so the rebalanced level design and better graphics make the DC version superior imo.
Of course the people who think the SMB games on NES and the SM All Stars versions are completely different games might disagree with me. The people who think the 5 versions of Guilty Gear XX are all unique games worth owning will disagree even more.
What is dislike about the newer two games, especially Spirits (DS) is that they don't really feel like a quirky action game anymore. They feel like a challenge mode for the main game, or like puzzle games.
Don't get me wrong, they are still worth buying and playing, especially considering how cheap they are. I just wish they were closer to the original, with more story, more "get from point A to point B where you kill the boss" action stages and less "you are in this room/situation, figure out what to do" puzzle stages.
Yeah, the N64 one controlled better, it even allowed to use the analog stick (in a practical way) for directional shooting, even though it doesnt take advantage of that since itīs only in 8 directions. But the digital scheme is still better than the Dreamcast one since the C buttons are closer to each other, allowing the thumb to rest easily in the middle and hold the buttons effortlessly. But everything that was improved on the DC aside from the controls is worth it. It is the version to get, but not the definitive experience since Bangai-O Missile Fury is coming and it features dual analog controls! Only the story remains to be seen, but quite honestly, it was so random on the N64 and DC games that I dont know if I prefer a set of levels like Bangai-O Spirits, which as a good game on its own.