I think Merlin have a clever marketing strategy in not having a "flagship" park.
Merlin carefully markets its resort theme parks, midway attractions and Legoland as separate entities. I think this method works well for them, especially given the location of their attractions. We could say that Thorpe Park is Merlin's "flagship park of the South", but I think due to different target markets, the resorts all hold their own very well.
Of course, all this goes without saying I think the Towers is the best
(Yet my 13 year old cousin thinks Thorpe always comes out on top...)