There is a parable of Jesus that talks about the importance of building a house on the proper foundation, so that when storms come, the house may survive. The unspoken implication is that a house built on a bad foundation, no matter how ornate and beautiful, is always at risk and plagued by instability.
That message comes through loud and clear in the third season of Chuck. I love the show, but the third season was not the equal of the first, and definitely not a patch on the delirious rush to the finish of season two. Many of the individual episodes were solid, and the execution and acting were very good, but long patches of the story seemed mired in cliche. There's a simple reason for that--exec producers Chris Fedak and Josh Schwartz made a fundamental mistake at the beginning of the season and no amount of hard work and talent could correct it.
Fedak and Schwartz ended S2 on a wonderful note. Sarah chose Chuck, his father had returned, all seemed right with the world, and then Chuck downloaded Intersect 2.o (or is it 2.5?). The awesome last line of the second season was "Hey guys, I know kung fu."
That's a heady peak. It would have been tricky to figure out just where to go from there, and NBC's dithering about whether or not to renew the show sure didn't help. Still, the route that they chose was the worst possible one--the Romantic Reset. Sarah was ready to run away with Chuck, but Chuck had decided he wanted to be a spy, and when Shaw (Brandon Routh) showed up... yawn.
Again, I'm not ranking on any of the actors. They all did yeoman work, even Routh, who many fans raked over the coals for being wooden. The problem was not the actor; it was the conception of the character. Shaw was so wrong, he was a seventh wheel. The notion that Sarah would waver between Chuck and Shaw was either ludicrous or offensive, depending on whether you felt it painted her as stupid or shallow.
The sad part is that much of what Fedak and Schwartz wanted to accomplish was easily within their grasp. Take a notion from the last six episodes: the power of the Intersect and its effect on a human brain. Start from there. Now S3 starts with Beckman pushing Chuck to find out the limits and capabilities of Intersect 2.0. After all, how do you download actual physical abilities into a human rather than just knowledge/data? Sarah believes this is a mistake, that Chuck is being pushed too fast, and Casey is on the fence. Now you bring in Shaw as an ally of Beckman. Now you have a web of conflict that doesn't revolve around the Chuck and Sarah romance. For extra spice, let's make Shaw a Ring double-agent from the jump, and as he tries to learn the secrets of the Intersect, he also attempts to drive a wedge between Chuck and Sarah. If you want another layer, Sarah becomes suspicious of her allies, since she sees them as insufficiently protective of the man she loves. Now she has real conflict and retains her strength and agency instead of becoming the victim of ginned-up, patently fake "romantic" conflict. Chuck's job in all this? Trying to understand and harness this new set of unearned abilities, a task that might be beyond him. This is possible if you just don't make the fatal mistake of assuming that you must reset Chuck and Sarah back into "will they/won't they/are they/aren't they" modality. Once you make that mistake, though, you're stuck with a flawed structure. It probably says a lot about the talent of everyone involved in Chuck that they were able to right the series as much as they did.
