At the other hand however some initial episodes during Season 1 are mediocre at best and it is a struggle to watch a few of them.
I would agree with this to some extent. There were some episodes where they were obviously still getting a feel for where the series was going to go. By the end of S1 they've really got it down though, and even the more mediocre episodes are fun.
I will certainly say this for Farscape: it's one of the few series with very consistent quality of storyline. The major arcs move forward at a good pace and the individual episode plots are very entertaining and move the characters forward. I felt that it got better with each season and was wrapped up nicely in the Peacekeeper Wars. It's a very satisfying viewer experience.