it arguably controls better on n64, but the sweeping changes in the game system make the dreamcast version superior. i thought the leveling system and the need to collect fruit to power up your super attack bogged the n64 version down needlessly. the streamlined dreamcast version focuses on the simple fun of throwing yourself into obscenely huge missile volleys and replying with obscenely huge missile volleys, over and over. the revisions just make it more enjoyable.
maybe my views are slanted by having played the dreamcast version first -- i enjoyed it enough to track down the purportedly better n64 version, and was disappointed.