I loved the ending. That was all kinds of awesome, numerous cuts or not. Casey's dumbfounded reaction was great.
I don't think kung-fu is going to be a permanent skill, but rather that the new Intersect causes him to react to each situation with the skills he needs to get the job done. In this case, he was surrounded by eight guys, so he flashed and recieved the kung-fu skills. Next time, maybe he'll go undercover as a botanist and he'll flash the knowledge necessary to play that role with credibility. I don't think they're just going to make him into a supersoldier, and I could see a lot of ways that a shifting knowledge base like that could be used for comedic effect, like turning him into a ladies man to seduce a rival spy. Moreso if, like the flash, he has no control over how he acts so it makes him do things he wouldn't normally do against his will, but he can still react to it as its happening like the geeky Chuck we all know and love (he was shocked by the kung-fu the first time he paused, so clearly a new persona doesn't take over as he gains the skills). Imagine if he's terrified of parachuting but suddenly jumps out of the plane completely against his will.
Plus, he'll probably keep his dad's nifty wrist computer to act as active support to Casey and Sarah on missions, so I don't see the dynamic of them taking the lead and him providing backup changing too much except in special circumstances.