I'm sure most people reading this page wish the show wasn't cancelled. Here is an article from Vanity Fair that talks with Paul Feig about what would have happened with the characters next.

Lindsay Weir (Linda Cardellini)
Paul Feig: I always figured something bad was gong to happen to Lindsay when she was out with the Dead. [The series ended with her ditching a summer-school program to follow the Grateful Dead with Kim Kelly.] I was hoping the second season would open with her being taken out of a concert on a stretcher while Queen’s “Tie Your Mother down” plays. That’s all I had. But I thought it would be interesting—she comes back, has completely lost the trust of her family; so she’s in even deeper having been really been outed as a problem. But there wasn’t a strong direction I had for her; I just knew she’d probably end up at some point in her twenties in Greenwich Village as a performance artist, and after that she’d probably become a lawyer—a human-rights lawyer.

Sam Weir (John Francis Daley)
Sam’s future was going to be drama club. Because that was my experience in school: I got deep into drama club. That was the storyline I was most excited about, because I was going to portray what actually happened to me. I thought he’d be more on the stage crew than actually performing, just because that was kind of interesting, the guys that were keeping it together from behind the scenes. But my drama teacher, who was one of the biggest influences on my life creatively, was an alcoholic, and over the course of my sophomore through senior year, she got worse and worse and started depending on me. I’d get called away from class under the guise of an emergency, and it would be her on the phone saying, “You’ve got to come pick me up. I left my car at the bar last night.” So I was really excited to get that going, this weird kind of taking-care-of-an-adult relationship, while he’s still learning amazing stuff from her, this tortured drama-teacher soul. That bummed me out the most, not getting to play that story out.

Neal Schweiber (Samm Levine)
Another burning desire I had was to get Neal into swing choir. Now Glee has taken it and run with it, but I always thought that would be a funny world for Neal to go into. There’s a weird little clique, and you have all these inside jokes, and all these kind of obnoxious performance things you bond with people over—I just thought he would really blossom in there and think he was kind of the king of the school. We figured it could be his outlet while his parents are going through a really horrible divorce. Since Judd had gone through that in his real life, that was kind of going to be his domain—telling all his tales from adolescence through that.

Bill Haverchuck (Martin Starr)
With his mom dating Coach Fredricks, Judd and I liked the idea of Bill slowly becoming a jock—that he turned out to be good at basketball and started to get into it, so that he was getting pulled a little more over to the jock side. Which would create an odd little rift with him and the other geeks. Because Martin is quite athletic in real life, and we were like, “Oh, let’s maybe play that out for him.” He works out a lot, Martin does, and at the beginning of the show he would come in with these giant biceps—we had to make him stop doing that.

Daniel Desario (James Franco)
Daniel’s such a drifter. I always liked the idea that eventually Daniel would probably end up in jail. [Laughs.] We were kind of, you know, taking him in this different direction. I wasn’t quite sure where that was going to lead. I knew it couldn’t stay in that world. I always liked the idea of: you go away for the summer and you come back and everybody’s kind of in a different place. But it’s hard to say with him; I think he had too many things pulling him in different directions. Having lost Kim, there would be a weirdness between them. But I wasn’t quite sure yet.

Kim Kelly (Busy Philipps)
I wanted Kim Kelly to be pregnant, but it wasn’t necessarily going to be Daniel’s. I thought this actually happened when she was out on the road with Lindsay following the Dead—that she shacked up with some guy, whether she was high at the moment or whatever, and comes back pregnant. That was another burning desire of mine, because when we were in high school there’d always be a girl or two who were pregnant, and it was so mind blowing. I thought it would be interesting with Daniel kind of around, and it’s not his, and it’s weird—and would he step up, since she doesn’t really know who the dad is, or isn’t really in contact with him? So maybe it was a chance for Daniel to become a young teen father—see what could have happened if we had a second season? And Kim and Lindsay—that would become a true friendship. Obviously they would have to have some back and forth and falling apart, but I like the girl power they had at the end of the last episode—they had both come through the fire in different ways and really bonded hardcore.

Nick Andopolis (Jason Segel)
I liked how we were kind of moving Nick towards having to go into the army, because of his badass dad. ’Cause that was a real option for so many people in my school—but he would be desperately trying to avoid it. But I was never quite clear exactly what direction we were going to go with Nick.

Ken Miller (Seth Rogen)
There was a guy I knew in school who was kind of Ken-like and he moved away to Hawaii; we were told he moved there just so he could smoke pot. I don’t know if that was the direction Ken was going to go. I always liked that we had set up that he had rich parents. But Ken’s such an enigma. I think he’s the guy that just kind of hangs around town. My instinct is we would have had the most fun searching for what his life would be. We liked to surprise people with Ken’s character—what was the thing you’d least expect he would do, or place he’d come from? I can completely see us loading him up with a lot of weird shit. I was sad we never got to show his parents, and God only knows whom we would have had him dating. I can definitely see a scenario where Lindsay would have tried dating Ken—that would be really funny. High-school romances are so flash-in-the-pan; there’s that awkwardness of having your ex walking around the school. Or, in my case, girls who turned me down but I had the awkwardness of them knowing I was into them and they had no interest in me.

Millie Kentner (Sarah Hagan)
We had actually thought about trying to turn Millie into a burnout at some point—“What? You’re what?” It would have been really fun to twist where she was going. I love changing people’s alliances. Because no one knows who they are or what they’re doing—basically they’re trying on different hats, different masks, if you will.

Cindy Sanders (Natasha Melnick)
We ended with Cindy as such a hardcore Republican. I liked her being a weird nemesis for Sam—I would have loved seeing them run against each other for student-council president. There’s nothing funnier to me than when the person you were in love with suddenly becomes this monster. You can’t figure out why you liked them. I think we would have had a lot of fun with Cindy.

Full article at http://www.vanityfair.com/online/oscars/2012/12/paul-feig-season-two-freaks-and-geeks