As a whole, Alton Towers is better themed, with proper themed areas that you can tell you are leaving/entering. Thorpe Park, it all just blurs into one, except Swarm island. But as this is the first time I've properly thought about it, Tidal Wave, Saw, Nemmy Inferno and The Swarm are all really good themed. In my opinion, The Swarm is the best- The station is really good, the trains are themed (Which nemmys aren't), the queue line is well themed and integrated (it feels quicker to me with the constant change of environment and the news reports) and there's lots of good scenery and near misses. The shops and toilets match, overall it's really effective.
But Alton Towers has more well themed coasters, just not the best, unless you look at rides collectively. With Nemesis, I voted looking at the theming around the coaster itself, not Sub-Terra. If Sub Terra was part of the build up and queue line for Nemesis, Nemesis would win (I would have the story that the eggs attack so you evacuate, only you take a wrong exit and end up running down to the tied mother who has woken up to protect her babies, then you are attacked by her)