Besides for attractions that are not receiving the attention they deserve my biggest problem with TDO is the merchandise that they choose to sell all around the resort. I'm not sure if they are the ones that ultimately decide what will be sold or displayed in the stores or if it is dictated to them from Burbank, but I hate how everything is pretty much the same. I don't like how they have all the generic merchandise in every store on property and either very little or no merchandise that is themed to the area it is in. I will admit that I do enjoy vinylmation, but there need to shove it in every store drives me crazy. I don't feel like I have been taking out of reality and placed in this amazing world when anywhere I go I see vinylmation everywhere, generic mickey t-shirts, high school musical and Hannah Montana dvds. I used to love Villians in Vogue because I thought it had cool stuff in it for villians, but now that store is basically just a Nightmare before Christmas/Vinylmation store with a boardgame with villians thrown in there.
Another pet peeve of mine with Disney is how they will sometimes use Walt's image and quotes to promote something, which doesn't seem to have any creativity at all in it. They need to all be put in a classroom and be taught the meaning behind the quotes.
This is something I feel Universal really excels at - keeping unique, relevant merchandise in its stores. Some examples:
*Plethora of Revenge of the Mummy-specific and Egyptian-themed merchandise in Sahara Traders
*Twister and farm-stuff in Aftermath
*Nickelodean stuff galore in the Nickstuff
*Some great, unique Jaws items throughout the Amity carts
*Tons of Men in Black/alien stuff in the MIB Gear
*Simpsons merchandise at the Kwik-E Mart
*Terminator items at Cyberdyne Styles
-Lots of specialty shopping at the Irish shop in New York, The Brown Derby, Oakley, etc...
-Spider-Man stuff at the... Spider-Man Shop (okay, maybe that name needed more work)
-Great, nostalgic comic book items and toys at Marvel Alternaverse
-A surprising amount of unique merchandise for some not-so-relevant characters at Toon Extra
-Great educational/entertainment based merchandise at the Jurassic Park stores
-Some AWESOME foreign and specialty items in the Lost Continent stores, such as Treasures of Poseidon and all of the carts in the Sinbad Bazaar
-Before Dueling Dragons left, it had a Dragon's Roost which sold an unbelievably cool amount of unique collectibles and apparel (I myself have two high-quality "fire and ice" dragon baby sculpts)
-Great Seussian items of all kinds and sorts in the various shops of Seuss Landing
-And now, with Harry Potter, a bulk of unbelievably cool unique items from the universe
...you'll notice each park has its own main store (Studios Store & the Islands of Adventure Trading Company) and Citywalk also has a main store (Universal Orlando Store) that sells a little bit of everything as well as your more generic Universal/Islands of Adventure items. Right now at Disney, all of the shops are like the Emporium, with the same generic crap lining every aisle. Disney could learn a lesson from Universal and perhaps sell some more quality merchandise.