While we'll probably never get anything official, the show's creator Zak Penn sent out a series of tweets containing the following highlights of what could have happened in Season 3:
http://www.summer-glau.com/blog/zak_penn_drops_alphas_season_3_hints/2013-03-09-738
Dr. Rosen lived. Hicks and Nina ended up together. Rachel went back to civilian life. Bill's kid was an alpha.
Gary ends up the leader of a reconstituted, less violent Red Flag. Parish dies of a viral infection that targets his peculiar chemistry.
Rosen ends up getting back together with his ex wife. They move to Binghamton, NY, where he gets tenure in the psychology dept.
Alpha abilities continue to evolve. The next generation can communicate with each other through non traditional means. It turns
out that they are heading towards a communal, hive like consciousness.
It has its pluses and minuses. Gary can't stand it.
Nothing wraps up too neatly. Being an alpha ends up neither blessing nor curse, simply different.
Hicks and Nina's kids are really good looking but a handful. Hicks falls off the wagon a few times. Nina pushes him back on.
Zooey [Zoe?] emancipates at age 12. Skyler [Skylar?] disappears one day and is never seen again. Dr. Rosen figures out the mechanism
behind Kats memory. She gains a long term memory, but loses her alpha
ability. Ill equipped to deal with normal life, hers ends tragically.
Zooey becomes a Senator, with help from Rosen. Later she turns on her own kind.
Rachel dumps John, ends up marrying an Orthodox Jew named Barry Shapiro. He is quiet and smart and clean. Rachel cheats on him a few
times
Bill starts meditating and goes back to the FBI.
Hicks's brother in law clears up his gambling debts. Cley gets a job as a high powered lawyer/lobbyist for a big energy company.
A guy named Barry Shump assassinates Gary Bell at a rally. Gary is 47 years old.
Bill and Rosen stay in touch. Rosen helps Bill with his alpha kids.
Gary accomplishes a great deal in his life. "Bellism" is coined to refer to underestimating people because of their neural differences.
Gary never does settle down, and he resents it when people suggest that he needs to be in love. That's their opinion.
An alpha named Mike Werbe ends up inventing a form of zip up one piece clothing that makes him a billionaire.
Dr. Rosen dyes his beard blue in solidarity with an alpha who is extradited to South America. (An all alpha country exists there.)
Also, to clarify, Hicks' brother in law is from his first wife. He has serious gambling debts.
There is still an active movement to get the third season done, so who knows?