I'd love to hear your thoughts on how you would have handled Clex's conclusion (the Smallville years anyway)! Of course if you're writing on this, no pressure to spoil what you're working on! Just fascinated with your take on things. β¨οΈπβ¨οΈ
Ooooh, this is an interesting question.
From a fic perspective, it largely depends on which au I'm working on. I try not to recycle too many plot points in their exact incarnations, and depending on what, specifically, I'm changing, it could really drastically affect the outcome.
As far as the show goes...I think the first major change I would make there would be actually letting Clark tell Lex his secret, because they would never be able to get together if Lex doesn't know. Not really. We already saw how Clark and Lana turned out due to that.
Clark doesn't have to tell anyone his secret, and I firmly believe no one should be trying to force him into it, not if they really care about him. But him not telling the person he claims to be in love with (in canon, that's Lana) is what makes their relationship toxic. Clark keeps a certain distance between them, and Lana is keenly aware that there's something major Clark isn't telling her, at least for a long time. There's other things that make their relationship toxic, but I think that's the original sin.
Now, back to the Clex interpretation.
I totally understand why, in Season 1, Clark doesn't tell Lex his secret. He literally had just met the guy, it takes time to really build up enough trust to be comfortable with it. But I think by the end of Season 1, Lex earns that trust. I think Clark would have told him sometime over the summer.
This wouldn't lead to them automatically dating, but I think it would allow them to build a closer friendship that would open the door to them dating later on. There are, however, two major things that Lex would probably wait for (and Clark may or may not be aware of).
The first would be for Clark to turn sixteen. This would happen at the end of Season 2, since his birthday is in May. I think Lex would probably place Clark into a mental "off-limits" box until then. Why then? Because Kansas' age of consent is 16.
The second would be for same-sex relationships to be decriminalized. This happens in June 2003 (Lawrence v Texas. Choix Libre sort of uses this as reasoning for Lex, because that fic is extremely grounded, and it works beautifully. I don't think in fics it's strictly necessary to, but for the show, I think they would have to). I think Lex would be aware enough to know his father would try to throw Clark under the bus in an effort to control Lex's life, so by waiting until then (he would probably be aware of the court case) he would be able to fight it. And it would also give Clark time to come to peace with the idea of liking boys.
So I don't think we would see an actual relationship start until at least Season 3. I think they would probably keep it discrete for a number of reasons, at least at first, things that look like their normal hangouts. I think Clark would worry his parents wouldn't approve, and while Smallville is canonically almost large enough to be considered a city (population-wise. If you've ever read Choix Libre, touchstoneaf talks about in the opening A/N of the first installment how as a town Smallville doesn't quite make sense), they are presented as a small town, and those tend to be extremely conservative, so letting the townsfolk find out could actually be dangerous for them.
I think once they do start dating it would really start changing things. Lex and Clark would then have additional, mutual support. Clark would have one less person to hide things from (a good thing, because Lex is involved in so much of it), he would likely be less anxious, paranoid, and depressed as a result, they would avoid being at cross-purposes (another thing that tends to happen, especially as the seasons advance), Lex would have gained more confidence in leaving his father's influence because he would have had the support to do so, and when Lionel gets possessed by Jor-El they would probably actually get to reach some sort of decent relationship, something Lex has always wanted.
Clex would have fixed pretty much everything.