I half wonder if the negative comments comments are because people are watching it in the mode of "This is comedy why aren't I laughing every single second".
I agree the show isn't laugh-a-minute. However I think it far more than that. I once heard this show described as "joyous" and I think that is a perfect description. This is a show that should produce joy rather than laughter. Laughter is reflexive and ephemeral while joy is more lasting and requires sympathy for the characters.
I enjoy the show because I love the characters. They may seem to be clichés but the are all archetypes in new contexts. We not only have meek nerds in dangerous situation but train killers in mundane situations.
I love watching these characters trying to adjust to these environments that are alien to them.
The other thing I like is that there is forward movement in nearly every episode especially in season 2. I'm so sick of shows that are stand alone bad-guy-of-the-week. Chuck has a clear story arch. It is a very plot driven show and secondarily a character driven show. The script is a formality much like Star Wars.
Really it is a classic story about man who is being forced to be the man he is meant to be. Chuck has the potential to be a hero but years as a lowly computer store clerk have obliterated his self confidence.
On the flip side it is the story of a girl who has been running around saving the world and just wants a normal life.
I guess if you don't have sympathy for the character you will never understand what is great about this show. It is FAR more than a bunch of spy clichés.
Another thing I love is the chemistry between Chuck and Sarah. It is more than just sexual tension the to characters are actually in love. This makes things a bit different to the usual sexual tension theme where the boy is trying to get the girl to like him. We know they like each other from the start. It is merely the circumstance that keeps them apart. This raises the stakes of the story arch of chuck trying to get the intersect out of his head.
In summary I believe you enjoy it more if you don't think of it as a purely as a comedy but as journey for the main characters.