And if a story is badly executed then I'm not gonna pretend it's well written even if I like the outcome as a concept. Just because the concept of "James is a sweet and supportive friend of Kara who never does anything wrong" or "Kara has a group of female friends rather than primarily male friends like in season 1" might be appealing as a concept to people doesn't mean that it can't be executed badly. And the show going "tell don't show" on us with Lena/James and Sam/Kara, were what the characters say directly contradicts what we as the audience SAW, is bad writing.
For the record, I agree that a huge problem of the Guardian storyline was that it never climaxed. It felt like it should have climaxed as him either giving up on Guardian because he learned his lesson that it was a mistake or it should have climaxed with Kara admitting in a big moment that she was wrong about him and that it's a good thing that he's Guardian.
The ending of the season felt like it sort of put in groundwork for the first option with the episode where James is upset that people are scared of Guardian, but then he clearly doesn't give it up. And he is still doing it this season even though we don't see as much of it. But he didn't get his proper moment of validation either.
So don't get me wrong, I'm not claiming that the Guardian arc was super well written. But to me it still very much fulfills the requirement of "characters having a life of their own". And compared to s3, it was, you know, an actual ongoing story rather than just random scenes that go on in the background.
IMO James still got meatier material in some of the Guardian episodes than he has gotten all this season so far, especially since imo the writers really screwed up James and Lena getting together. It just feels like they couldn't care less if they don't even bother putting in a minimum of romantic buildup. Again, maybe this will change, but we are a third of the season down and it's pretty frustrating to me that if there's supposed to be a story there that it still hasn't really started.
But to me that is more a sign of the bad writing of season 3 than a complaint against he bad writing of season 2. If s3 didn't want to continue the Winn/Lyra storyline all they would have had to do was to drop us a sentence that they broke up, it's not like there was no groundwork with the arguments they had the last time we saw her. Just like they still haven't told us what happened to Lillian Luthor after the s2 finale. Did she go to jail? Is the on the run? Was she exhonorated? To me those are all examples of the bad, careless, lack of attention to detail writing that s3 is riddled with and that shows up in the writing of all the supporting characters.
And I don't see how "Alex was gay, but in self-denial" is a bigger out of the blue wtf than "Alex has always been obsessed with being a mom she just never mentioned it ever before". So it's not like s3 isn't doing their own share of "cheating" with characterization.
As you said, it was a thankless task but he got screentime and got to express emotions. Which to me beats the thankless role he has this season where he is there for Kara and gets rewarded by Kara telling a character she had 2 conversations with that she never had a best friend, but she has best friends now in Lena and Sam. => two people she's constantly lying to because she doesn't care enough to share her secret with, while she couldn't wait to share it with her work friend Winn in season 1. It just feels like the show is trying to pull the wool over our eyes to FORCE this storyline to fit, but they don't actually want to put in the work to build it up.
Which is exactly why s3 imo suffers from A LOT of bad writing, even if the general focus and themes of the season might resonate with you more. I just want better attention to detail writing and it bugs me that they are so bad at that in s3 when they used to be better at that in s1 and even in s2 as well.