I think the reason that we didn't see Gobo and Boober together a lot is because their personalities would often put them in conflict with one another, leaving writers very little to go on to move the plot forward.
Gobo is the leader, go getter, adventurer, explorer-type; willing to do almost anything if there is something new to see and something great to explore
Boober is the antagonist in a sense where he is definitely NOT the ok let's do it type fraggle. He sticks to only doing things he is comfortable with, unless a friend of his is in danger or if he knows the activity is in the best interest of the group (even if he doesn't want to do it.) A lot of stories between Gobo and Boober would be: Gobo: Hey Boober, let's go see ______; Boober: "No way! Definitely a guarantee for death and pestilence, and I wouldn't have time to do the laundry!"
With conflict like that, there is not a whole lot writers can do with that to get rid of the conflict. We saw it a few times during the series, but there were just better ways to showcase the characters by matching them up with other fraggles.