I agree that the biggest problem with Season 4's start is the absence of Aeryn and Moya. They had to find a way to introduce the new characters, so I think it makes sense to not have them distracted by the John/Aeryn story right away, but it can be a bit rough.
I'm exactly where you are right now, bigdaddy
, and while I do enjoy those episodes now, I definitely remember how annoying it was sitting through them the first time around.
At least you can just blow through them on your DVDs. I had to watch them one week at a time. It was over a month before Moya was even back on the screen!