I think Chuck has made many of the same mistakes that Lost made, in "revealing" the "big picture". But I don't really care so much in the case of Chuck... it's not that I don't like Chuck because I like it quite a bit. It's just that the show has always been more about its texture to me, than its substance.
Whereas I think the substance of Lost was more important to me.
So, yes... lots of groan worthy and convoluted contradictory elements on Chuck... but it's just fun so I just go with it.
And it has Timothy Dalton in season 4.