Hmm... this actually wasn't bad. I'm not totally buying Samuel's motivations, but at least we have a plot and some progression of said plot. That was my main problem with the season so far. Nothing happened on a pretty regular basis and 75% of the show had nothing to do with the final plot that wasn't really revealed until now. They could have easily made this plot line become a half season volume like Generations, Villains, and Fugitives and then every episode would be jam packed.
Now, I wouldn't want to keep the show in the status quo, but some of the elements that really worked from earlier seasons was how the plot was driven. You'd find out a little bit each episode until you saw everything at the end and it all made sense. The audience knew about the bomb, the Shanti Virus, Pinehurst, and Building 26 with in the first few episodes, but not all the puzzle pieces were in place. They used things like Time Travel and Issac's paintings to fill in those gaps until the whole picture was there. Up until like last episode, I had not clue what our Heroes had to stop. That's not good story telling.
Also, where are our main characters? If I'm not mistaken the main characters for this season are Hiro, Ando, Peter, Nathan, Angela, Noah, Tracy, Claire, Matt, Mohinder, Samuel, and Sylar. This episode, the penultimate episode, only featured five of them. That's less than half and the way things are going, I doubt we'll see the rest of them before the end of the season. Now, I think the fat should be trimmed a bit. I know Nathan is gone, so that's one. The plot lines for Mohinder, Tracy, Angela and Sylar have all dried up. Hell, the way this season is going, I'd argue that all of their plots have dried up, but the show wouldn't survive without some of the mains.
Sylar needs to die. From Season 1-3 to now, he's like a different character and I'm not sure that's entirely a good thing. When he came to be, he was scary. When he showed up, you feared for the other characters lives. He's been meandering for a while now and now that he's "good" again I feel like they just have to kill him. I'm perfectly okay with him having redemption, but not living as a Hero, because I know he'd just be back to being a villain again and the writers would try to chalk it up to be the coolest thing since the show started...
My idea for the last episode is for the Heroes to have like a "one step up, two steps back" kind of thing. Part of New York City is lost, but Sylar prevents the whole city from being lost and at the same time is killed. But most importantly, the general public learns about people with abilities. Not just the government or scientists like Suresh, but everyone. The next season can take place like a year after this one and deal with the ramifications of the public knowing, perhaps having them go underground or something to that effect. If they are intent on keeping Claire, throw her with Peter. Let's face it the best Claire scenes from ever season are when she's with Peter. Or maybe keep them all together for once (or mostly together. Where would the fun be if they were all in one place?) Ultimately... DO SOMETHING DIFFERENT!