I will take the argument from the other side. Good old Jean-Luc Godard used to say that you cannot make a great movie from a great book, so you better pick a mediocre book. The idea behind this is that for a book to be great, it must use the specificities of its medium, so if you try to port it to another medium, some of its greatness will be lost. A great part of what makes Cowboy Bebop work is the postures. movements and mannerisms of the characters that are possible with the codes and techniques of animated cartoons. You can use these codes in live action films with special effects (and many films do - while based on a comic book, Scott Pilgrim vs The World comes to mind), but that gives a feeling of artificiality that is often not there in the source material.
A great example of this would be Ed. Think about Ed in Cowboy Bebop and how the character moves, the unexpected ways the character enters and leave the frame. This is nigh impossible to do in live action and is destined to be lost in translation or feel super weird...
Other than this, character and environmental designs that can work in drawn/animated form very easily look super campy and cheap in live action form and if you attempt to tone them down to make them more "realistic" you often just make things look bland which is not much better. In the specific case of adaptations made in the US, you also often have the problem of a re-writting that does not understand the qualities of the source material or is done with the assumption that staying close to the original plot, tone and themes would not be palatable for a wider occidental audience. So in the end, you have a good chance to end with something that looks weird, campy or bland and that has been gutted of what made it interesting in the first place... so yeah. Not to mention the source material can also very well be extremely dubious!
On a more optimistic note, for decades there has been very good movies based on manga. Lone Wolf And Cub in the '70s come to mind, but closer to us, we can mention Our Little Sister (a family drama film by Hirokazu Kore-eda) or Blade of the Immortal (swordfighting film by Takashi Miike). It's my understanding that the movies based on 20th Century Boys are nice also. Good movies based on anime though.... nothing springs to mind, but not that many anime are original work themselves.