WMG / The 4400

Promicin caused the dystopian future.
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.

Dennis Ryland is one of the marked.
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)

Shawn's abduction went exactly as planned
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.

We're only seeing the newest iteration of the timeline.
The factions of the future are in a never ending fight over the past. Each time one side wins the other undoes it. Hence why their plans are so convoluted - they're really a tangle of moves and counter moves. This is supported by the episode where the good (?) future people take the children and send them further back, but by the end of the episode it's undone.

The reason Kevin's healing was so convoluted when they could have just taken him and healed him themselves is because originally they did, and something went wrong, but both sides still needed him so it was accomplished in a different way. The reason the ripple effects could be so planned with such ludicrous precision despite the inherently chaotic nature of human behavior is they've been done dozens, maybe hundreds, maybe thousands of times. There can never be peace for the 4400 and their loved ones and the disaster can never be averted because every time the good guys win, the bad guys will just fuck it up again.

Kevin has the starzal mutation.
No evidence for this whatsoever, I just really want him and Tess to have adorable super powered babies.
http://tvtropes.org/pmwiki/pmwiki.php/WMG/TheFortyFourHundred