Throughout the series, there's a constant uncertainty about whether the 4400 and other people with powers wind up causing the brutally divided future world they were supposed to prevent. Fair enough. But in the original timeline, promicin would have been invented in a huge government lab instead of discovered in the brains of abductees, and that would have been even more dangerous. The first test subjects would have been soldiers, making up superpowered special forces similar to what we saw on the series. With time the superpowers would have spread up the ranks and into the government, perhaps also to wealthly private individuals too. Giving superpowers to people who were already powerful would be the perfect recipe for the kind of divided society that our heroes were warned against. The whole 4400 project is an attempt to spread out the superpowers to ordinary people. First through the abductions, then through the promicin injections, then through the contagious version. Jordan Collier may sound creepy but any similarities between his plans and the dystopia are a coincidence.
think about it, during his absence he seem to have gone through a major personality change, he is doing everything in his power to limit promicin, and Isabelle, the marked pet project, seem to decide to help him out for no reason, she probably have some kind of instinctive attraction to her creators that make her want to help them (as long as it doesn't interfere with her life)
Future!Kyle said the people from the future wanted Kyle and Shawn interfered with it, and that's why Kyle ended in a coma and Shawn had to go back with Healing Hands to fix him. But Shawn does a lot more than it, including being Collier's second hand and substitute when Collier's killed, gaining a lot of support for the 4400 thanks to his cures, and lots more of stuff, so it's either a great improvisation or planned all along. Besides, all 4400 whose abductions are seen were taken when they were alone, but Kyle and Shawn were together, so it's logical to think the people from the future wanted something from both.