Indeed, they did an admirable job on that front right up until the Mystery Marriage, which is so nonsensical it goes a long way towards overshadowing the organic relationship trajectory that had preceded it. In hindsight, I would easily endure a few cliché roadblocks along the way if it allowed me to avoid such a clumsy obstacle once the characters fully committed to a romantic relationship. It's such a shame; they avoided so many typical pitfalls for three years, and then dove into a uniquely bad chasm rather than staying true to a natural path.
True, that was the one truly ridiculously stupid thing they did. I still don't know who thought of this or thought it was a good idea. However, it was at least a uniquely stupid path, rather than the same worn out path other shows went down. So I can live with the stupidity, while wishing they'd found a more interesting way of dealing with their marriage.
I suppose one could call Amanda naive in the first couple of seasons, with regards to the world of spies, but clueless? I don't think so. She had her own way of figuring things out or getting the job done, and that's so the opposite of clueless to me.
Well, she was a little clueless when it came to being tailed in the beginning, and then falling for the idiotic line of Alan Squires in "Artful Dodger". Then there was that weird thing on moles in "The Mole." I think it's not that she was clueless in general, but more specifically about certain aspects of the spy world. She had really good people skills and a knowledge of normal life that Lee never had, so he was as clueless about her world as she was as his.
Although the show had them have an organic romance, I still felt like the showrunners were playing mind games with us: were they dating in Season 3 or weren't they? That episode, which one was it--where the Congressman was murdered with a bomb in the baby's carriage? At the end of the show, how Lee said they should have dinner and no "shop talk this time", which led me to believe that they had had several dinners--but it's so ambiguous and vague.
They just seemed...so much more comfortable with each other; but then again, we had "Utopia Now", which contradicts some of what happened earlier in the season.
I think part of the problem is that the beginning of season 3 was a bit of a mess, since they initially planned one thing and then went with another. I think in a sense that Lee and Amanda drifted into dating without really knowing it. The impression I'd gotten from the "no shop talk" thing is that while they were working they'd often eat together and talk over the case, but this time, Lee wanted something more personal, especially since he makes it a point that he'd rather be with Amanda than Leslie. So that's what made it different from the other dinners they'd had together.
And I think the other problem is the episodic nature of 80s television. It's a miracle they managed to get anywhere at all. Because it does seem weird that Lee would almost kiss her in "Sour Grapes" and then give the Speech again in "Utopia Now". But on the other hand, Lee having major mood swings between episodes is actually in character for him. So if you go with the idea that he's a bit skittish about the idea of where his and Amanda's relationship is going, and Amanda isn't exactly sure either, then the contradictions could be kind of a push/pull of "is this a good idea or bad idea?" kind of thing rather than the usual "will they/won't they" thing.