That's like saying if Joyce complained of a headache in Season 1 then the signs were "there" that she was going to get a brain tumour and die. When something is written before the fact, and the fact wasn't even thought of yet, then you can't say that the something was written with the fact in mind.
What I meant was that if you were to just look at the show itself as a complete work of art/literature, while ignoring authorial intent (death of the author and all that) then one could easily read back and forth and make connections and interpretations that were never intended by the writers. It would be like novels that were originally released in serialised form - the works of Charles Dickens for example. Originally he was writing them in instalments and would take into account his audience's reactions and modify plot and character development. When we pick up a copy of his novels today however, we read them as one complete piece of work and can read into them what we see for ourselves.
Like I said, serialised TV, and Buffy especially, is much more complicated because there is really no one author and stuff changes constantly. Despite Joss being Plot Overlord, characters were written differently by each writer, and because of the age of the internet the choices the writers made in response to fan reactions are far more obvious. There's also the element of actor performance, especially where JM brought more to Spike than anyone ever asked for. It's actually why I find it difficult to disconnect author from text with Buffy (and AtS) because the logic and continuity fails are sometimes so glaring so you can't help but feel the sense of contrivance.
Having said all that, I think the key to the 'Spuffy in S2' issue is really the inconsistency between Lover's Walk and FFL that you rightly point out. That is a retcon plain and simple because the two just don't match.
To go back to answering the original question, I think Spuffy did have chemistry, just of a different kind. Because Bangel was about intense first love their sexual chemistry was tender and virginal, especially as it was largely about Buffy's blossoming teenage sexuality (although I believe they could have explored this a lot more in S3). Aside from that Angel's silence and stability worked well against her rambling and emotional highs and lows and provided her with the comfort and sense of balance she craves. Their physicality in one another's presence is also easy and more relaxed.
SMG and JM do play off against each other really well and I think Spike and Buffy are at their most enjoyable as frenemies who are constantly fighting and snarking. I do also think they had sexual chemistry in S6, which is why Smashed does work well. I think James carries it more because Spike is so obsessed with Buffy and he plays it very well, whereas with Bangel SMG carries the ship more because she identifies with Buffy better, she's a more experienced actress than David, and because we see the relationship from Buffy's point of view rather than Angel's. I don't see a romantic tension with Spuffy (certainly not a balanced one, you could say it's there from Spike's POV) because up until S7 that's not what it was about. The tension is physical, and palpably
tense, because of Buffy's depression and her need to feel something, which I reckon Sarah conveys a lot with her eyes. There is a noticeable connection between them, although the kind understanding they share in the latter half of S5-first half of S6 I personally found OOC because I find nicey-nice selfless Spike confusing.
It's so strange reading the parallel thread on the Spuffy forum, where fans have made almost exactly the same arguments against Bangel chemistry as people here have of Spuffy! [Ship name] is melodramatic/forced/lacks romantic chemistry; [Ship name]-their bodies are drawn to each other; [Ship name] lacks sexual chemistry. Weird. I guess we're back to square one!
