I think part of the problem is that they try to tie to many of the episodes into the arc. I think it could also work if they spread out the arc over a handfull of episodes throughout the season, instead of every single episode. So they could give us two or three arc episodes, then two or three standalones, then more arc episodes, repeated until the end of the season. So kind of like what you guys are talking about with Enterprise Season 4, but do it as one arc in bits and pieces rather than small arcs.
Looking back over the Season 2 episodes, I see there were more standlones than I originally thought, but even most of them still had elements tying them back into the Zoom/Jay/Earth-2 storyline.