I think it's difficult to talk about Cowboy Bebop. Easy to say something good, exact and precarious otherwise. Because you'd better have your shit in order if you're gonna criticize.
Common criticism:
Weak story line
Too self-loving ("The work which will become a new genre itself.")
In the first, they're missing the point. The second is grasping at shadows.
It's undeniable that Cowboy Bebop is one of the greatest works of anime. Nearly every aspect is seamless. Cliche free, plot hole free, budget-cut-animation free. (No harem, gratuitous fan service, gratuitous moe, whiny male lead, unbearably irrational characters, cheap or overwrought plot devices.)
The universe isn't so foreign, neither are the character types. But there's nothing quite like it, and certainly nothing similar that stands up to the shear force of quality, diversity, originality. In that sense, it's pretty damn sui generis.
So most talk falls in the white noise range: Like? Y/N. Because of gushing pukes like myself, enough people have taken to disliking Cowboy Bebop on obstinance rather than merit. Not that Cowboy Bebop is impregnable, but try to come up with a different anime (fuck, a different anything) that does it better. Cowboy Bebop isn't something you can dismiss with a finger wag, eye roll, upturned nose. By all means, it's not chiseled in the universe to like the anime, but an offhand comment isn't nearly enough. Fiction this great earns an exit fee.