Another great show, now onto my opinions on the subject (again, anything I don't have enough experience or opinion with is getting skipped):
I definitely agree with you guys on this one, the Disney Animation building is much cooler in Anaheim than it is in Florida. The first time you walk into the room with all the screens surrounding you it's a little bit breathtaking, and by contrast the Florida version has become not much more than a glorified meet and greet area. As a lobby for the surrounding attractions the Disneyland version works much better.
Animation Academy and Sorceror's Workshop are similar enough on both costs that I'm not going to spend much time on them and skip straight to
Turtle Talk with Crush:
I agree that the surrounding environment is cooler at Walt Disney World (in fact The Seas with Nemo and Friends was one of my favorite attractions in Epcot), but for the same reason I gave Disneyland the edge with the Jungle Cruise, I'm choosing the DCA version over Epcot's. The performance of Crush, from my experience, is consistently much better at Disneyland than it is at Disney World, again, I don't know if it's just that LA has a larger talent pool than Orlando, or if we were just unlucky enough to get all the stinkers, but I almost always walk away from Turtle Talk at Disneyland with a huge grin on my face, and the same cannot be said for the WDW version. If the WDW version had consistently better talent, it'd be the obvious winner, but as it stands I prefer Disneyland.
I don't agree with the sweeping statement that Mike made regarding Disneyland attractions just feeling dumped into the environment rather than properly integrated, but I will agree Muppet*Vision at Disney's Hollywood Studios is a much more complete experience than it is at California Adventure. There are some gags at the DCA version that aren't present in the WDW version that I enjoy (the disaster effects props to name one), but it doesn't compare to the surrounding Muppet theming that is present in Florida. Walt Disney World definitely has the edge here.
Twilight Zone Tower of Terror:
I quite like the Disneyland version, I think it's interesting in that it's a unique experience from the Walt Disney World version and thus there's a compelling reason to see both, however, at Disney World it has a more complete package. Both rides are fun in their own way and I couldn't necessarily choose one over the other, but at Disney World you feel much more immersed in the attraction because the queue and surrounding area are much more elaborate. Its location at the end of Sunset Blvd. is great and it visibly looms over you the entire time you're in that section of the park, the grounds are wonderfully dilapidated and overgrown, and fake elevator doors in the lobby line up properly with the direction of the elevators on the exterior of the building. The California version, just doesn't have that same dramatic flair upon your approach, and the dummy elevators in the lobby are perpendicular to the elevator shafts which has always driven me nuts. Both are great, but Florida has the edge here.
Monsters, Inc. (Mike & Sully to the Rescue vs. Laugh Floor):
Laugh Floor is entertaining, but I don't feel it works as well as Turtle Talk with Crush. It's fun, but in my opinion it's only really worth doing once per trip. Mike & Sully to the Rescue, I'd say, is a much more fun attraction, however, given the film it's based on it has the potential to be much much more. I understand that they were trying to salvage the terrible Superstar Limo as inexpensively as possible, and in that regard they did a remarkable job. The fact that they were able to transform the infrastructure of such a truly god-awful attraction into a charming ride like Monsters, Inc. is nothing short of incredible, but it doesn't match the scope of what's seen in the film. I'd love to see them completely reinvent the ride to be much more elaborate and exciting, but since we all know that's never going to happen, I'll just have to make do with a good attraction that didn't have the ambition to be great. It's still better than Laugh Floor though, which was the original point before I got off on a tangent.
Toy Story Midway Mania:
This one's tricky, I think the queue at Disney's Hollywood Studios is really neat and definitely more entertaining than the fairly standard queue at California Adventure, but, I think the Disneyland version is integrated into the surrounding area better. Yes, Disney's Hollywood Studios has the surrounding Pixar Place area, but since there's nothing else in that area except the attraction it's little more than an elaborate facade for the building. At Disneyland, Toy Story Mania was the first step in transitioning the theme of Paradise Pier, and it is now very well integrated into the surrounding area and attractions, and it feels much more natural there. Also, the Mr. Potato Head barker is much more appropriate outside the attraction drawing people in, rather than tucked away inside where, by the time you see him, you've already committed twenty minutes or so to the queue making his barking a bit superfluous. Also, while the becoming the size of the toy aspect is obvious and in your face in Florida, Disneyland's version accomplishes the same thing in a much more subtle way by showing the ride as a play set in a Victorian decorated room at the exit of the ride. The over the top nature of the Disney World version is definitely cool, but I also appreciate the subtle simplicity of the California version. It's a tough call, but I'm going to say Disneyland here.
Games of the Boardwalk/Dino-Rama:
I think you guys summed it up pretty nicely: Games of the Boardwalk are reminiscent of a Victorian sea-side amusement park with a Disney twist, and Dino-Rama is reminiscent of a shady local carnival. Disneyland wins for understanding that "shady carnival" is not exactly the best theme to go for.
Mulholland Madness/Goofy's Sky School vs. Primeval Whirl:
When I got off Primeval Whirl I thought to myself, "wow, what a massive waste of space. Not only do you have an extremely mediocre attraction, you have two of them for the price of one." Mulholland Madness is an equally mediocre attraction, but at least it has the decency to take up half the space. Disneyland is the winner here, and I'm hoping that the Goofy "How To" theming will make it more enjoyable as well.
Walt Disney World is so big that it's hard to do everything on one trip, and sadly Kali River Rapids was one we had to skip on our last trip, so I'm going to skip this one.
Redwood Creek Challenge Trail vs. The Boneyard:
I really enjoy Dinosaur (as I mentioned in the response to the first episode in this series) but Dinoland, USA is, in my opinion, kind of crappy aside from that. There's no consistent theming to the land, and you have cartoony two steps away from scientific without any kind of clever transition or integration. The Boneyard is a perfect microcosm of this. It just feels kind of jumbled together and not very well thought out. Redwood Creek has the edge here for having a consistent theme.
Soarin' (Over California):
Disneyland's is integrated much better than Walt Disney World's is. With or without the last two words in the title, it's still obviously Soarin' Over California, and that works much better in California. It also works much better in the setting of Condor Flats than it does in the setting of The Land.