Oh, I did, too. However, when the first half was originally airing, I just remember being a little frustrated by the fact that the episodes had so little to do with the main story arc.
Ah but that's the thing - they actually did have plenty to do with the arc, just not in ways everyone immediately understood or expected.
It's best summed up in an episode, I forget which, where the crew split off into two groups because they feel they can't trust each other, and then proceed to outline exactly the same plan, even predicting some of their own reactions.
That would be "Wait for the Wheel," where they're trying to save Moya from the Pathfinders.
I'm just getting up to the part where Scorpius keeps popping up in John's imagination saying things like "you'll never see the trap until it's closed". What foreshadowing. I want to know what happens now
Seriously though don't spoil me.
Ooh - "Beware of Dog," one of the creepiest episodes ever, and the best use of Harvey of them all.