I really like your theory about Walter's dream, it's very imaginative, though unnecesary. As Walter said, unconscious mind usually works while the conscious one sleeps. I've found solution to several problems while sleeping, so it doesn't surprise me what happened to Walter. Mind works in some strange ways and is powerful enough to find solution without external help. But I really like your theory.
Jones definitely is not a "good guy" (he's done so many evil things) though maybe his goals are well-intentioned. Creating a whole new universe just for fun seems too excessive, even for a guy as megalomaniac as Jones. He has to have more powerful reasons. Preventing the war against the observers seems a good one. Or maybe he causes the invasion. Because he's creating new species, and Observers are evolved humans. Can Jones' genetic experiments the key to the birth of the observers?