Topics like this are very hard to comment in. Firstly because so much has happened in the last decade, so just listing all the cock-ups is no easy feat. Then to decide on a 'winner'?
Anyway, I think that for me Hard Rock Park should get a mention. It was easily one of the worst park failures in the last decade. I thought the park has so much potential, but it just didn't work! Even after they sold the park (I think that's what they did, I don't remember exactly), it still didn't work and finally they just shut it down. Massive shame and a huge cock-up.
Merlin? Not so sure about this. I didn't really visit the parks very much before they were Merlin owned, so it'd be hard for me to compare. Merlin certainly have done some odd things though!
Any specific coasters? X/X2 possibly, but from what I've heard the new version is great so...
Furius Baco possibly? I've got a feeling the design of the trains was slightly rushed (massive speculation I know, but). The launch is absolutely incredible, and the layout had so much potential, I LOVED the ride the first time I rode it in the middle at the front, but after a few more rides you finally realise how rough it is. It's such a shame because it could've been so good. Having said that, I wouldn't really say it was the biggest cock-up of the decade.
The final one, and it's something that I think would make the Six Flags park ten times better, is the bins for bags and stuff on the station platforms. I honestly can't understand why they can't have them and frankly it annoyed me, so for me that was a big cock-up.
Like I said above, you could keep picking out specific examples all over the place, so I'll stop here.