I might be in the minority but I enjoyed some of those episodes. I think it was the angst, which I enjoy. The pain in Clark's face or the musical montage in one of those episodes (can't remember which one this early in the morning).
Think of it this way, they worked so hard to be together and everyone has obstacles, this is just one more obstacle they had to overcome. Not everyone has evil Lex Luthor's or amnesia, or doubles, but they have money, jobs, addictions, and so on. Lois and Clark came out stronger at the end for what happened.
