Both are keepers in my book and it is hard to compare them as they're very different playing games as people have already illustrated. BSD is a very difficult short, point-based game, MSF has longer ball times, but is mode-based and some of the modes are a real challenge.
The artwork/presentation are far superior on MSF, but I feel the audio work and theme are cooler on BSD. Gameplay is great on both.
If you held me at gun point and I could only keep one, though, I'd have to go with MSF. Only game prettier from the DMD era is TOTAN in my book.