If there is a next season, one thing I hope for is that they connect more characters together. That was one thing I felt was a huge mistake in every season after S1. At the S1 finale, every character came together in Kirby Plaza. Then by the S2 premiere they were all scattered everywhere again, and one of the major problems of that volume was way too many plotlines. I know why they did it: they wanted to rehash S1 instead of changing the format of the show. I think that was a mistake and I really think more characters should have come together.
Though I have a sneaking suspicion that they reason they avoid having the characters come together is because the writer's can't write for more then 4 main characters in a single plot line. If you pay attention, you'll notice everytime the number of characters present goes higher then 3 or 4, characters will have a poorly written excuse to leave. Like in Volume 4 when Hiro and Ando decided to go India for no reason instead of helping Matt, Peter, and Mohinder take down Building 26. Or in Volume 5 when Hiro, Mohinder, and Ando ended up Noah's apartment and Mohinder decided to forget the whole Samuel thing and just go back home to India (I guess he is his father's son, they both created a monster and then decided to ignore it and let it run around killing people). That stuff just annoys me.
What do you expect? Haha you can't fit 15 characters in one episode. This is one of Heroes' biggest mistake(s). They need to trim down to more quality characters versus quanity. Yeah it seems they ditched the whole idea that everyone is connected. I think it's safe to say that we can do without Claire, HRG, Suresh, Tracy, Hiro/Ando right now and focus more on Sylar, Peter, Matt, Mama Petrelli.
Downsizing the cast would be a plus because it would leave them availability to introduce new stories, new characters! I don't know if Samuel's story should continue into a new season. I liked the character but just like the show, it really didn't go anywhere.
The show needs stronger villains. I also think turning Sylar into a good guy was a huge mistake and a let down for me. It's not believable for me and I don't know if they can even have him be a villain ever again now. The show is convoluted and contradicts itself each week due to poor character development and writing. They truly are scrambling for ideas.
I strongly believe we might see these characters develop a second identity like a Clark Kent, Bruce Wayne, Peter Parker sort of thing if the world DOES know about these people with abilities because of Claire's leap of faith. How that pans out might be interesting. The power to reveal a good guy's true identity or a bad guy's identity, while not entirely original, it's always been a cool thing to play with.
Maybe they can have Peter continue being a paramedic, saving people. Maybe Sylar can become a doctor and heal people with his powers? Who knows? Matt Parkman becomes a cop or FBI agent again and tracks down people with abilities or maybe he gets a job with the secret service to protect the president who just so happens to be a powerful villain?
In the end, I agree, scattering each character is not good for the show. They need to keep them together and connected whether through good intentions or bad. It doesn't matter.