Since I had some free time recently, I had a chance to rewatch those first 13 and I noticed one thing about especially Shaw/Sarah romance, it didn't really matter, so I found it funny that ppl seems to be so fixated on the storyline (the less they showed it, the more obsessed ppl were about it) that was so totally secondary and frankly unimportant in grand scheme of things, also on purpose underplayed by Chuck writers (Fedak in interview said well before Chuck season 3 premiered that Shaw is not really someone that stands between Chuck and Sarah, there are other issues that are far more important).
If it was important, then they would develop Shaw better, who was nothing more than plot device character, so the only reason for this romance to exist was to illustrate that Sarah is moving away from Chuck the more immersed he is in spy world, to have Sarah character to talk to, so we see her own journey better and to create a character for Chuck to kill down the road. I think ppl were just used to the story being about Chuck vs other guy in previous season, so even when the story was different this time, they were still treating it the same way as before.
It was never about Shaw vs Chuck in terms of fight for Sarah affection, it was always about how Sarah percieve Chuck and the moment she saw there is still him aka "good Chuck" behind his new spy persona, it was "bye Shaw" the exact moment, so the angst with Shaw was mostly created in ppl heads. Like I said ppl fixated on the storyline that TPTB treated as relatively unimportant to the story and that recieved little of screentime because of that.
There was some problems with the story obviously and I focus mostly on more "technical aspects, since if the story was "worthy" is smth of personal preference.
First of all Shaw was on way too long for a plot device character and an actor was badly miscasted, because he couldn't carry clearly underwritten role with his mere presence and charisma ( and he had very little of that) + I doubt he was suppose to come off so stiff and charmless.
Second of all there was some rushed storylines, Mask being main example (big jumps in storyline), there was also some structure problems in those middle episodes. I remember reading how in Mask ppl complained how Sarah said he liked neck kiss, when YS played the scene that Sarah was clearly uncomfortable.
Some said YS must have not played it right, but the answer is far simpler, Sarah was lying to Shaw, she didn't really liked it, but still was opening possibility for romance, why she was doing it, well, that was a question and the Mask episode should have given some glipses in her reasoning (and imo that was mistake for TPTB that it didn't, the structure of that story was not right), but we had to wait for that until next episode and there we were given good explanation, why she was moving on.
The same thing was during Final Exam episode, ppl were saying that it was story error, that Sarah told Chuck they can't be together if he leaves spy world, why ppl can't accept that she was lying to him too (and YS played that line the same way as when she told Shaw she likes neck kissing, she sounded a bit unconvincing - I rewatched those scenes few times back to back). She had an order to give him an assigment and if she said the truth, it would have been easy way out for Chuck and she clearly wanted that his decision should be about him own morality and not about her.
And the last fault, imo the most serious, was the whole storyline was created on thin premise that characters are not communicating + one character had to remain passive (mostly Sarah) and since the story was streched to 13 episodes, it really became bothersome and hurted both characters. So overall the whole arc has some faults, but fortunately individual episodes are mostly good, with few truly great ones.