Cowboy Bebop, and here's why:
The characters have much more depth and are fleshed out with much better pacing. In SC, Fuu just seems rather annoying most of the time, while Jin (while having a decent backstory) just doesn't seem beat-up about any of it, and I don't think Mugen is quite mad enough. In fact, the only character I could identify with was the blind girl who was bitchin' with a jumonji yari (and once again, God, those people scare me).
The action in CB was better spread and had arcs that ranged from sneaking about to all out pounding matches that felt satisfying regardless of when in the series it was. However, once you got past the first four episodes of SC, the action just died for another six/seven episodes as it devolved into all levels of silly (the Jin impersonator/eating competition etc.).
The seiyuus for Bebop were much better, each bringing an individuality to the character. And while I don't mind Ayako Kawasumi, she just made Fuu sound like a spoiled brat, and Ginpei Sato could've been replaced by a machine for all anyone cares. (However, I would rather have had Aoi Tada do her 'Ed' voice from the film, because it was so much more eccentric.)
Won't say anything about backstory stuff, because I reckon they both cover that very well. Same with most of the bit part characters. So instead, having three central characters is always difficult to pull off in a half-year season, especially when one of them is effectively an automaton. CB introduced Ein, Faye and Ed along the way which allowed the series to flow much better.
And here's the kicker: Ein. The best animated dog in existence, seriously, who wouldn't want Ein as their pet, huh?
