I prefer B5 overall, although it suffered because of the battle JMS had to make the suits realise that he was doing something ground-breaking and because of the adjustments he had to make with the actresses (losing Takinawa, then Talia, then Ivanova ahead of schedule, and the problems Julie Caitlin Brown (and other actresses had with the prosthetics). B5 also failed to capitalise on several interesting female characters (Sakai and Timov spring to mind). Season 5 definitely suffered because the Earth War finale had to be crammed into Season 4.
While it was often a tad too manic (thank goodness for Aeryn Sun to keep things a bit muted), Farscape took more chances with its characters, including the inspired idea of splitting them onto two different ships at one point. I also loved that Farscape was so visually striking, had a lot of really good roles for women, and put more effort into making aliens more alien (although I absolutely love the Vorlons and Shadows).