SPOILER ALERT if you haven't finished the series yet...
...but a large part of me thinks the series should've ended with Kaoru actually dying, as opposed to just seeming to die.
The author of the manga even mentioned this in one of his writeups, claiming the main reason he let Kaoru live is because shonen manga should end with smiles and a happy ending. He was 50-50 on the choice of whether or not to kill Kaoru for a while.
But the means by which they kept Kaoru alive are pretty patently ridiculous. I was reading the manga thinking, "Ho, damn, things are getting pretty dark... but there's no way Kaoru can be not-dead, right? Like, her corpse is right there on the page." So then of course they pull some ridiculous bullshit about some really skilled dollmaker just made a facsimile of Kaoru's corpse, and Enishi couldn't bear to kill the real Kaoru because bla bla bla sister complex something. Really, guys?
And thematically — it arguably does work better if Kaoru were to die. The ghosts of Kenshin's past as a hitokirki, the idea of justice coming back for him, the idea of finding a way to repent for the sins of the past... All that would be pushed to the forefront with an event like that.
Though... there's some themes that would be squashed with that kind of ending. Though ending with Kaoru's death would feel less contrived and more brutally honest/real, Kenshin was never quite the same feel as, say, Cowboy Bebop. The inevitability of having to deal with one's past actions and the affect of the past on the present were big players, but so too were the ideas of redemption, the warmth within Kaoru and Kenshin's pseduo-family-unit, and so on. If everything had ended with Sano leaving, Kaoru dead, and Kenshin dying of despair in the outcast village, it would've been a huge letdown. It'd be the vanquishing of Kenshin's sakabatou and his vows. Bebop could pull this off because the whole series, you had a sense that Spike was running away from something, and you knew things couldn't end well when they came back for him. Kenshin, on the whole, despite having similar themes, had a much more optimistic overall feel.
Kenshin's an interesting series in that it balances these competing "dark" and "light" themes throughout.