I enjoyed the season finale, and look forward to the wrap-up. It appeared that the "ending" was likely an alternative, shot in case the show was renewed, hence the harsh editing. I suspect they had a "that's all, folks, thanks fans!" type ending should renewal have went the other way.
Of course there's always the chance that Chuck "defeats" the cliffhanger (since he always wins), and the season ends with next-to-nothing dangling in the wind, story-wise.