Dude .... I started to reply to some of your posts, but I need to re-read the things myself again now I think, in their entirety, before doing so.
But yes ..... I think if Fringe took off in the direction the comics started going, it may have stood another couple of years at least. Less "who is Peter going to screw" arcs and more history/sci-fi/wtf arcs directly. The Fresh Start Soap Company would have been awesomeness in the show. Arguably, it's parallel seems to be akin to Kelvin Genetics.
I'm going to try and re-read them over the next few days ... I have hard copies of all of them, including the prequel (squees just a bit) ^_^