Structurally, "The Wish" is pretty much a mess. It begins as a story about how Cordelia copes with the breakup, and it looks at first like the world-without-Buffy concept is going to stay rooted in that story. But not long after we arrive in the alternate reality, Cordelia is killed and the story meanders off in other directions. Of course, by the end of the episode we return to Cordelia and her plight, but none of it ever really connects together.
"Oh, the Bronze isn't cool in this reality. I've got to make these little adjustments."
But the episode works anyway because Cordelia's death is sufficiently surprising and the Wishverse is interesting enough, and slowly learning about the way things are in this world is certainly compelling enough to justify a twenty-minute digression. It's fun to see the Master and his Order of Aurelius again: even while they weren't fantastic villains in season one, the fact that we now have a new perspective on them and their plan from season one makes them more interesting. It's also kind of fun to watch the protagonist role pass from Cordelia to Giles to Buffy; the abandonment of a sensible structure actually compounds the sense that nothing can be taken for granted (which has been an important tenet of the show from the opening scene of "Welcome to the Hellmouth."
If there's a unifying theme to this story, I think it's a bit more complicated and subtle than "be careful what you wish for." It has more to do with the assumptions that Cordelia makes, particularly with regard to the way she chooses to assign blame for her situation and the way she sees cause and effect at work in the world around her. When Cordelia wishes Buffy had never come to Sunnydale, she's making some pretty self-centered assumptions about the way the world works, as though Buffy's only function is to cause misery for her. But by wishing Buffy's arrival in Sunnydale she causes things she never anticipated.
And some of these changes are easy to foresee, but some aren't. The notion that Willow and Xander are vampires isn't too hard to swallow, nor is the idea that Giles is trying to fight the vampires even without the Slayer. But it's hard to understand why Giles' group of "White Hats" in this world consists of Oz, Larry, and someone we've never heard of called Nancy, and no justification is given. Which I think is great. There's no way anyone could have anticipated that, and that's pretty much the point. So overall, even with its oddities, the episode offers something pretty interesting.