I was thinking about this exact thing the other day when I was looking over old Alton Towers maps. I'm 25 and have been visiting the park since I was 7 years old (1997), and have always been a huge enthusiast.
Looking back to maps of the park from what I would personally consider its 'glory years' of 1998-2003, gave me a feeling of excitement which I can remember from when I was that age, thinking of travelling through the park on the monorail seeing all the rides, studying last years park map for weeks before my visit, that is exactly what I define as the so called 'magic'.
Now the question of weather or not this is gone I think comes down to two things; firstly, I've grown up. I'm 25 now not 12. I'm not saying I can't get excited about things any more but I certainly don't think it would be normal to get that same feeling from a theme park that I did when I was young.
That said, I have to wonder if as a 12 year old now, if Alton Towers would create the same magical feeling it did for me back then, and to be honest I think it would, but probably not to quite the same level. There is no question that they have gone downhill since the halcyon days of Tussauds in the 90s and early 00s. The park then really seemed to have a vision of what they wanted to do. This is probably the influence of Wardley and others but they really seemed to care about the detail, and want to rival parks like Disney for the overall experience.
I think the loss of magic can be seen in things like CATCF's cardboard exterior compared to the pink turrets of Toyland Tours, sticking a random space ride at the end of Forbidden Valley, or a racing theme in UG Land. The level or care which went into things like Storybook Land and Katanga Canyon won't be seen again any time soon. The focus seems to have shifted to individual, unique and marketable experiences opposed to consistency and immersion.
That said, I do think that being a child I would still feel some of what I felt back then going into Alton Towers now, and maybe a lot of these shifts are just a sign of the times rather than failings of Merlin.
So I do think the magic has gone, a little, but I think that was always going to happen to a point, for me anyway, considering how obsessed I was with this place as a child.
Long post I know but it is something I feel quite strongly about!