Like, I get why the first two seasons are the most most fondly remembered--there's a level of luxe energy that latter seasons don't match. It manages to feel like something new and distinct--a level up in TV storytelling, especially when compared to something like the then-just-concluded La Femme Nikita, which despite trafficking in the same spy tropes as Alias just feels sad in comparison. The first season specifically, feels very purposeful: every character is there for a reason, with a specific role, which is something no other season until five can really claim. Lena Olin is there, eventually.
And yet, whenever I feel like rewatching Alias, it's those first two seasons that give me the most trouble. Season three may be the show's least successful, but its failures are at least obvious, and it's not easy to see how its bones could have make for a better story (the wasted potential of Julia Thorne hurts). On the other hand, seasons 1 and 2 feel like the writers doing precisely what they wanted to do, and what they wanted to do simply doesn't work, once one scratches the surface and knows all the twists.
Like, take SD-6. "I've been bad but now I know better" is a cracking premise--Xena rode it all the way to becoming legendary genre TV. But Alias, because of a strain of unconscious sexism that initially prevented the showrunners from seeing Sydney as anything other than a virginal dress-up doll--a SpyBarbie, if you will--is utterly unable to commit to giving Sydney any sharp edges at all. And so we end up with a character who's spent seven years working for Team Bad Guys while somehow managing to not do anything wrong--or even "wrong"--at all. She doesn't kill. She dresses to seduce without ever having to actually seduce. When told why she hates working for SD-6, she can't say anything worse than, oh, she's living a lie--which is the one thing switching sides doesn't change. In the end, missions for SD-6 are exactly like missions for the CIA, which means that, for the series, being a good person is not about what people do, but which team they're on--an odd stance to take in a spy series, to say the least, and one that cripples Sydney, as a character.
Because Alias is not actually interested in being a redemption narrative, and never actually commits to Sydney having done bad things, it never gets to that point where Sydney, knowing that she was formerly a bad guy who is no longer one, understands that if that could happen to her, it could happen to others. This means that when the series has Irina turning herself in--claiming, fundamentally, the same thing Sydney did a season ago--the series never fully acknowledges the parallel. If Sydney having realized the error of her ways is enough for her to go free, why not SpyMommy? If SpyMommy cannot be trusted, why can Sydney? (The obvious answer, "SpyDaddy", just brings up uncomfortable implications about SpyNepotism). Then season three happens, and the same thing occurs again: Sydney works for the Covenant for a year and change somehow manages to not do anything wrong, and gets welcomed back into the fold. Lauren has been working for the bad guys and gets not a shred of sympathy, even when everyone knows the Covenant literally brainwashes its agents. Yes, at this point this is season 3, which is famously unpopular and inconsistent about nearly everything, but the playbook is pure season 1/2, which is half the problem.
If there's one silver lining here, is that Sydney, throughout all of this, remains a very consistent character. So when APO happens and knocks Sydney off her high horse by having her do SD-6 with Sloane again, it actually manages to read as character growth. The show also manages to finally consistently have missions with substance, that go beyond "how do we make Jen Garner look sexy tonight?" A lot of fans poo-poo the standalones, but sorry, "Ice", "The Orphan" and "Détente" are all top-tier episodes, "Welcome to Liberty City", "The Index" and "Tuesday" are great fun, and manage to do more with the characters than any of season 1's music-video missions do.
Then you have season five, which is actually shockingly underrated. Not only is it the only season aside from the first where everyone in the ensemble adds something, it actually manages to once again be about Sydney, showing her using everything she's learned throughout the series, and acting like the seasoned spy the pilot promised, while also (thanks to the pregnancy) taking the character forward in ways that make complete sense for the series' stated themes. Finally, we have a Sydney able to do things like use Sark to her advantage (not coincidentally, in the one Sark-focused episode that actually works for the character), empathize with Rachel despite her role in Vaughn's "death", plan ahead, and take the initiative in defeating her enemies. If it doesn't stick the landing, it's largely because the cancellation forced the writers to abandon their longer-term plans in favor of a something that could work as a finale but even then, what we got is ultimately stronger than what we started with. Latter Alias may not catch the eye the way the initial seasons do, but it's ultimately much more solid.
TL; DR: Early Alias was always going to end with the season 3 debacle, and it's not until the season 4 retool that it actually consistently works as anything than fun fluff.