Seasons 3/4 move past the "alien of the week" (though occasionally they have one still) and get into a more episodic season long arc that I think fits a lot better.

If only those effects were a little bit higher quality.

Oh man, are you in for a treat, that show improves so much from the end of S1 on after Scorpius shows up.

If you end up liking it, definitely also check out the 1970s BBC sci-fi series Blake's 7. Farscape paid tribute to it in many ways, including the 'fugitives on a spacecraft fleeing through the galaxy' element. There's also a later villain, Grayza, who looks remarkably like Servalan, the main villain in Blake's 7.

That said, Blake was far more serious in tone.