How exactly can you fuck up continuity in comics? It's fluid. Focus on what the story is about and not so much on how it connects. That line of thinking probably doesn't help Smallville's case much, though.
My room mate who has watched every episode almost religiously said he liked it as an ending for the show, but not as an ending for several of the plot lines. He also said it felt like they were setting up something to happen after ... and now it never will.