The season finale aired on Monday, and it was great, in my opinion it should have done enough and showed possibilites for next season enough to be picked up. That being said, the writer have to have to have to acknowledge what they did through dialogue of the show.
At the end of this season Chuck gets uploaded with a new and improved intersect that now gives him the ability to take down a whole room of Fulcrum agents because evidentally the new intersect uploaded the knowledge to do kung fu. That is fine it opens up a load of options for season 3, how will chuck deal with his new abilities, how will sarah feel about him as her equal, etc..However, the writers have to acknowledge the similarity to the Matrix.
Chuck needs to actually bring up the Matrix when talking about what happend to him, and his new Neo status, cause if they do not acknowledge it then they will be running away from the fact that they used that device striaght from the Matrix, if they talk about it then they are part of the joke and it is ok, then it is just like life imitating art, but things like using the line "I know Kung Fu." which is literally word for word the thing Keanu Reeve says in the Matrix, leads me to believe they will present it in a coincidence jokey way, in which case it is cool. But the writers put themselves in this corner, so they need to be proactive with it and allow Chuck to revel in his new Neo-ness.
That is of course assuming that Chuck gets picked up for a third season which they better, cause lets face it, what else does NBC have to hang their hat on. Besides The Office, Chuck is literally the only NBC show I care about in the least. In my opinion, they need to bring it back, and put it on a different day, facing off with The Big Bang Theory and How I Met Your Mother is not doing it any favors. Put it on Tuesday where hardly any good shows air, and see if it can not get some better ratings. Its a great show and deserves to continue. I would much rather have this than any Elderly Dating Show, or whatever the next stupid reality show they will come up with next.