Said it before, say it again:
Season 2
Give Peter's amnesia-kaitlin-whats in the box-paint the future-get chased by Elle-lose Kaitlin-get duped by Adam storyline to Gabriel Gray.
Let Matt and Nathan be dead. Subplot where Candice replaces Nathan in his life and eventually 'becomes' Nathan, even in her own mind. Matt Parkman Jr. becomes an important baby for some reason or other.
Feature the 12 as the focus of the paintings as opposed to HRG. Set Peter and Monica (granddaughter of one of the 12) on the discovering the twelve storyline that Matt and Nathan had, and lengthen it.
More action in Feudal Japan, including Hiro learning sword fighting. Hiro and Adam split when Adam wishes to take over Japan so that he can use to to save (take over) the world. To remove Hiro from comic relief world, less Ando for now.
I'd put Mohinder, Jessica, Molly and Micah in Mohinder's apartment together, just trying to get by and live a normal life... y'know, except for Mohinder trying to take down the Company. Mohinder would betray those three, not HRG.
Maya and Alejandro would replace Hiro and Ando as comic relief, and would meet people along the way every episode (ie Meredith, Claude, Micah, a new guest star, perhaps someone from the online comics, one of the 12, Candice/Nathan, etc)
Claire would trust West, who would betray her to the Company eventually.
Include the "1975" Flashback ep.
Build up to a battle between the Original Generation (Adam, Bob, Angela, a Kaito-possessed Ando, and one more) and the new generation (Peter, Sylar, Claire, Monica and Hiro) - The OG have lesser powers but know how to use them a lot better ie Angela using her precognition as spidey-sense, Bob transmuting air in front of him into a diamond barrier, etc...
Season 3
Go a completely different direction, either do the Virus storyline in full.
Or do "Villains" like "Heroes," that is, ordinary people with extraordinary abilities who end up, through various vices, weaknesses and failings, trying to take over and destroy the world instead of trying to save it. Do six new "villains" who start out as just waitresses, cab drivers, firemen, physicians, gamer teenagers and retired bookies.
If we HAVE to follow the way they went, then the jailbreakers would all be utterly badass and at least 4 would have real depth. Sylar would be more of a pent-up animal the Company uses than someone who reformed and stuff. Claire would be teamed up with someone else, likely Mohinder or something. Hiro would be traveling throughout time, interacting with other characters similar to how LOST flashbacks and flashforwards work, where he weaves in and out of others' storylines, giving all of us a bigger picture of the universe and the connections. The would be no 'powers formula' storyline ,and the 'villains' would be doing nothing short of taking over the world 'for its own good.' Gabriel would obviously not be a Petrelli, there would be no Tracy, Elle would still be a psychopath... y'know, don't break the universe-type stuff. They symbol would still be everywhere (not just on people's logos, but in the background of stuff) and there would still be that ubiquitous "Hero" being tossed around dramatically.
And as a bonus:
Season 1
For the finale, the six combatants would encircle Sylar, he'd redirect both Matt and Claire's bullets back at them, Sylar blasts Peter into Nikki before dodging a slice from Hiro, freezing his face so that he has to claw at it, and making an ice puddle under his feet so he falls on his back. When Sylar goes to blast Nikki with radiation, injured D.L. grabs his heart. Sylar soars backwards and DL lets go as he flies through a wall. Peter gets Nikki's superstrength and tells her to go protect the kids and begins to Wallop on Sylar, Peter's hands glow and he looks at them all terrified. Sylar laughs and begins talking about how Peter is the bomb and how Sylar came here to stop him because "You're the problem Peter. I'm just the bad guy." and proceeds to try and choke the life out of him. Hiro interupts and before Sylar can kill Hiro, DL phases into his body, holding him in a seizure and calls for Hiro to strike. After a short protest, Hiro does so, killing D.L. and apparently killing Sylar (cue Micah: "Daaaaaaad!")
Peter's meltdown then continues as it appeared.
Also, I'd imply, say by Charles Deveaux, that there are different kinds of time travel, "that Nakamura boy's already done two or three." to explain why Hiro's Five Years Gone time travel rules are different from his "October 2, November 8" time travel rules...