I'm personally not a huge fan of the long story arcs. While I loved the new BSG, if you missed an episode it made it very difficult to watch the next one.It is probably tougher to write alien-of-the-week, than to take one concept and spread it out over 13 weeks.
I think a couple of small arcs might have worked, like making the year of hell several episodes instead of just a two part. Also I think that year of hell would have been better as the season finale