I had seen Ninja Scroll, the Movie first before I watched the series version. The gap was about a year and a half apart, and I thoroughly enjoyed the movie despite its mature content.
The series takes place after the movie's storyline, obviously. But I'm disappointed in its lack of strong structure or character. Two rival clans compete for total power as they try to capture a girl and a magic stone necessary for the task, and Jubei and friends are caught in the middle. That's just what it's all about, really.
Especially after seeing the breathtaking action sequences of the movie, the series has a little rusty version of those that left me a bit jaded to be honest. The characters aren't that well developed, Jubei also lacks a lot of character, the animation is not as vibrant and alive as the movie. The bottom-line is that I don't think there is anything new or interesting to be seen here, regretfully speaking. It just tries to parrot the movie : violence, "sexiness" and stuff; and is doing a bad job at it.
Word of advice : if you have seen the movie first and are about to see the series now, I told you so; and if you have seen the series, but haven't yet seen the movie, go see it NOW!! Thirdly, if you haven't seen either of them yet, definitely go for the movie, trust me!!