Alton Towers just win. Look at areas like Katanga Canyon, Forbidden valley..You see my point.
At Thorpe I didn't really feel the sense of escapism and its not really themed as most areas just look the same. The swarm island is a much better than the rest of the park but not good enough to make me think Thorpe Park is totally and utterly better than towers.
If Alton don't put effort into themeing then why do we have Nemesis.. That didn't happen over night.
In fairness though, all of the areas and rides you mention were before Merlin took over, and before Thorpe got any serious investment. I'd say since the turn of the millenium, Thorpe has generally had the better themed attractions. It may not have themed areas as Alton does, but then Alton has far, far more land to work with.
If you compare recent additions directly then there's a solid argument to say that The Swarm is better themed than The Smiler, Saw is better themed than Th13teen, Colossus is better themed than Rita... and so on.
That being said, size of park shouldn't be a factor that restricts good themeing and development. Chessington is small and captures the feeling of escapism far better than either Alton or Thorpe in my opinion.