Things did get disjointed at the end, with Mandrakk appearing out of nowhere unless you read Superman Beyond, and the two parallel narratives in the last issue, but up to that point it was remarkably straight-forward.
People were already saying they were lost with the first issue, though, and my theory is this: They were lost because they were expecting to need to know more than they actually needed to know. In a lot of cases, knowing the background of an obscure character might enhance your appreciation of a scene, but isn’t actually required to understand it, but readers who are used to recognizing everyone might have been put off by the gaps in their knowledge.
I had a theory at the time that the more knowledge of the DCU you have, the more lost you would get with Final Crisis — and a casual fan would probably have an easier time following it!