The Doctor Who Experience was slightly different to what I was imagining but an advancement of the story section
The experience was great, I loved it and visited it every year (first in London and then its home in Cardiff Bay) but ultimately it was just an excuse to see the props and things from the show (don't get me wrong, I loved that too and it was a shame we lost Llangollen's, Blackpool's, the original Cardiff Bay one and the touring exhibitions) and the actual walkthrough was more a experience through a Doctor Who story (similar to the current War of the Worlds Experience (or whatever it is called in London, which is also fab))
I'm thinking of it as a light scare maze but an actual maze. The shows roots are basically monsters running down corridors. The TARDIS has landed on an unknown planet and the Doctor (a version from the future) has been captured. Captain Jack etc is trapped but you've been selected as the rescuers. The maze then opens up, Daleks etc hide around in the dead ends, chasing you out through different sections. The original experience part of the Doctor Who experience was a little bit of a let down really, it wasn't the full potential it could be.
I've also thought a weeping angel drop track coaster would work quite well. Imagine in the scene room, lots of flashing lights and the weeping angels popping up and when they get close, is when you've been transported in time