My first suggestion to enhance Cowboy Bebop is to take out the following episodes: Heavy Metal Queen, Toys in the Attic, Mushroom Samba, Wild Horses, Pierrot le Fou, Boogie Woogie Feng Shui, and Cowboy Funk. These episodes are fun (except for Pierrot le Fou), but slow down the momentum of the underlying storyline. Also, these episodes are well crafted, like the rest of the series, but end up feeling like filler.
The rest of the episodes can be left as they are. I originally considered dropping four more episodes, but they actually contibute to the general understanding of the Cowboy Bebop universe. Asteroid Blues sets up the mood and setting of the series. In Sympathy for the Devil, the Moon "acident" is mentioned. Waltz for Venus is a heartfelt episode that reflects some of the new issues for humans living in the interplanetary age. And in Brain Scratch, which seems like a filler episode, we see some interesting traits from Faye and Spike.