It's a big cliffhanger.
Most of the plot threads are resolved, but a new one is introduced that isn't. And this one would have overshadowed all the others, if those had not been resolved (which just made the season itself annoying because this new problem was building for most of the season, but focus was on everyone else).
For completeness, I'm going to include a summary for everyone else under spoiler markup:
The Patriots were dealt with. They had done so many things in order to take control, that the main characters were able to do a kidnapping and put on an act to get one of their commanders to admit it aloud. A representative of the Republic of Texas was watching the act from the sidelines, so he could see the truth. The Texans then broke their alliance with the Patriots and took them out.
The Nano has become sentient, and is now trying to impose order upon all life on the planet. But it's slow going - so far, it has made fireflies blink in unison, rats run in circles (similar to fish in a tank), and several humans repeat the same single action forever. The basis for the actions programmed into the humans were from old magazine advertisements, because in the advertisements, those humans looked happy. Aaron was unable to convince it that they were fake emotions.
At the end of the series, Aaron and Rachel have directly opposed the Nano, and decided it must be destroyed. The Nano on the other hand has been building an army - using images of dead loved ones to convince certain humans to converge on a single location, the only location it has decided to restore electricity to.
Later addition:
Well, it appears the cliffhanger ending will be dealt with! Starting on May 4, DC Comics will be releasing digital comics to tie up the story. According to the show's creator, Eric Kripke, it will be tied up the same way it would have had the series continued on TV.
