Eh, I didn't have many big issues with the the Ds's D-pad over anolog stick controls. The DS's touch screen simulates the Nintendo 64's anolog stick, so if you really hate the D-pad, you can you use the touch screen. SM64DS also has more characters to play as, more stars to collect and more courses to explore. However, none of these extra courses are major levels like the other 15 levels, but it's nice to have something to do after beating all 15 of SM64DS's levels.
Also, SM64 didn't have MultiPlayer. Okay, Multiplayer in SM64DS wasn't big, new, or immensely interesting, but it's still good for some quick, harmless fun for you and your friends. Plus, enhanced graphics are always a plus.
In conclusion: SM64DS is the definate buy. SM64 for the Virtual console is basically the same thing as SM64 for the N64, while SM64DS is a widly improved version of the classic game.