The production itself. The music was incredibly chosen and no expense was spared in chase scenes. They even filmed the series, rather than videotaping it, to give it a more theatrical look. The simplest explanantion is that ABC cancelled the show. Moonlighting was one of the most expensive TV shows to produce while it was running.
Television is, after all, a business.
If this explanation sounds too simple, well that's because it is. ABC eventually got tired of it too. Many actresses have been pregnant and given birth without it affecting the show. This case was different. This was a show that had one or both stars in almost every scene.