IMO, there's not a single thing at DHS that even comes close to touching the perfection of Jaws. Its one of my favorite attractions ever. I will agree that Shrek is a bit lame, but its not like the Hitchcock show that was there before was fantastic to begin with.
I also don't care for Jimmy Neutron, and while my nostalgia side says that Hanna Barberra was a better attraction, I also realize that nobody aside from adults today even knows who any of those characters were. The ride system at that is the problem, as it is very dated, not the film.
I'll also agree with you that Twister is fairly lame and I much preferred The Ghostbusters show.
That said, I don't agree with anything else you said. Was I sad to see Kong go? Definitely, but he wasn't drawing lines anymore, and Mummy is fantastic. Would I have preferred to received mummy and kept Kong? Of course, but losing Kong for Mummy wasn't a downgrade.
Men In Black didn't replace anything, and the ride is fantastic. The theming is wonderful, the queue is brilliant, and the ride is fun. You may not like the movie but that doesn't mean the ride is lame.
Yes, Simpsons replaced Back to the Future, but its a slight upgrade still. I know there were those who were fond of BTTF, but it had gotten very dated. Adding the Simpsons was fresher and has breathed some life there. To me the ride system is still a bit dated, but its fun. And The Horror Makeup show is probably the best show in all of Orlando.
Is USF a perfect park? No, but the comparison is to DHS which is just a mess. Yes, DHS has some nice theming and two top notch rides, but that is it. Star Tours is in major need of an update as is the Great Movie Ride, Toy Story is ok, but just a low D ticket ride, and everything else is either very very dated, or just needs to be replaced. Add to the fact that DHS has no unifying direction and it fails. One or two good rides does not a park make.
So if the question is which park has the single best ride? I'd go with DHS. But the question is all in all, which park is a more complete, better experience. For that its USF at least in my opinion.