I have a feeling that every park is getting the "new logo", and yet no park is losing their original.
What I mean is that in "official" stuff (or relatively print-based areas where a graphic logo may look out of place such as embroidery on employee hats, sweatshirts, printing on employee water bottles, etc.) would have the new standard company-wide font with the flags for dotting the i's.
Meanwhile, graphical pages on websites, sell-to-the-guests apparel, souvenirs, etc. will have the more graphical-type logos we've been used to for years at each individual park. It would help to distinguish the employee in the eyes of the guests from the other guests that just happen to be wearing the apparel they bought in the park since the employees would have the corporate image (which everyone knows they are BIG on corporate image).
That's just my speculation - I haven't heard any rumors one way or the other yet, though.
Cedar Point is the flagship of the chain, and always will be. Heck, the reason the company is called 'Cedar Fair' in the first place was when CEDAR point bought vallyeFAIR. It doesn't strike me odd in the least that the new company-wide logo would incorporate elements (i.e. font and i's-dotted-with-flags) from Cedar Point, and then just tack on the CFECo somewhere around it.
What confuses me about that Carowinds brochure is that they've taken off the "Crocodile Dundee" part of Boomerang Bay, but kept names like Top Gun and BORG. But it seems like they're keeping Nick, at least for now, since it's all over the brochure. And I don't think the new logo looks that bad. It's better than the Paramount ones in my opinion.