I've always been told, it's not the story, but how well you tell it.
Aelita, Jeremy, Odd, Ulrich, and Yumi have strong personalities and well-defined backstories (even if we aren't privy to all the details). They don't do things in a vacuum and neither do their adversaries, whether we're talking about Sissy, Jim or Xana. (Although I'm still trying to figure out what jobs Jim hasn't had in his past . . .

)
If they ever decided to do novels or anthologies based on Code Lyoko, I'd be one of the first people applying for a slot. The world is well-crafted, logical in its own way and yet, there are still a lot of areas to plumb (What ever happened to Sam? Does Odd really live with his grandmother, or was that just a ruse at the airport? Who are some of the other kids we see and how do they interact with our heroes? What do the teachers do when they're not in the classrooms?)
While there's a certain amount of formula involved in Lyoko (just like in Sailor Moon, Voltron, or any other "adventure" story where they have to defeat the villian before the end of the show), I see a flexability in the show that's not quite like the others mentioned. These characters seem to act more like real people (they fight with each other, they grow as people, they fall in and out of love . . . ).
I think the way the writers deal with the characters and make fighting Xana almost secondary to the story is Lyoko's real strength.
As always, your mileage may vary with these opinions.