The Bourne movies are all convoluted and have too many characters and get confusing. Mission impossible movies (especially 3-5) are all badass and have amazing action sequences. They also keep getting better. Mission Impossible all the way.
I like both of those action movie franchises. I'll give a slight edge to M.I. on this one though. Perhaps because it is based on one of my favorite TV series growing up.
FYI - M.I. 6 is filming now. Will release next year.