It's a hard question to answer, because the show has changed over time, and there have been things it's done well at some times and dreadfully at others. I've made my opinion clear that I consider the past three seasons to be virtually a different show from the previous seven. Things it's recently done well that it used to do badly include:
* Moving Clark toward his destiny. For seven seasons, Millar & Gough kept his development arrested, fighting his maturation toward Supermanhood at every step of the way, but immediately upon their departure, the show began moving him toward an embrace of his superhero role -- at least, insofar as they could given the core premise that he wouldn't become Superman per se until the end of the series.
* The music. Mark Snow's scores were awful, just droning, whining atmospherics. The only time he did anything melodic was when he quoted John Williams. But since Louis Febre took over as composer, the music has improved immensely, becoming much more melodic and thematically driven. Now, if only they'd ditch that unbearable theme song and let Febre do a full main-title arrangement of his proto-Superman motif.
If there's one thing the show has done more or less consistently well over its entire run, it's giving dimension to the main villains. Lex Luthor in the early seasons was a very rich, complex character, and he had a great relationship with Clark. Lionel Luthor was a similarly engaging figure. Both fell prey to the deterioration in the show's writing in the middle years. But the post-Millar/Gough show has managed to recapture some of that. Whereas the comics' Doomsday was a terrible, shallow idea, nothing more than a lame plot device, the show turned Davis Bloome/Doomsday into a complicated character, a sympathetic antagonist with an engaging arc. And last season, the show created a version of Zod that was as complex and nuanced as Lex had been in the early seasons, a friend-turned-rival to Jor-El paralleling Lex's relationship with Clark. Like Lex, Major Zod was a character who had the potential to go either way; you could see the potential for good in him, so it made his villainous destiny all the more tragic.
As for Chloe, I can't entirely agree that the show did her well. She is a good character for the most part, but much of that is due to the casting. The problem is, the writers insist on trying to give her a hip, witty, pun-laden dialogue style a la Joss Whedon, and they are simply terrible at it. Most of her glib dialogue over the years has been achingly bad and I've felt sorry for Allison Mack for having to spout such stilted, unnatural, unfunny lines all the time.