I've never liked the idea of soul mates, either. The whole concept grates on me. Then, on top of that, we have to accept reincarnation.
Even accepting those two concepts for the sake of the show, Lois, Clark, Tempus, et. al are stuck going through the same thing over and over again. There is no growth or learning based on previous lives - they're just replaying the same roles. By the time they've reached their most recent incarnation, even Sisypuhs would be looking at them with pity.
Then there's the curse. I suppose I should be able to accept the curse idea, but I question H.G. Wells timing. Waiting until after their third attempt at getting married finally succeeded? Why didn't he show up as soon as they were engaged? Or at any other time prior to their marriage?
Now, when it comes to fanfic, usually I try to stay away from "soul mate" stories because the idea grates on me so much. That said, I've read several that I actually like. Some of them I've liked despite the soul mate aspect, and the story would have worked just as well or better without it. Others I've read actually hinge on the soul mate idea, but they're well enough executed that it doesn't bother me.