Since I flip flop on the order, here's my top favorite and top least favorite in no particular order:
Favorite:
The majority of the African Savannah, especially for the Kudu/impala, baboons, lions, cheetah, exception being elephants which I feel is too small, though I'm aware there's far worse elephant exhibits.
Malayan Woods Pavilion
Australasia Pavilion
African Rainforest
Tundra Trek
Least favorite:
Indonesia, both indoors and out (with the exception of the Lion Tailed Macaques), especially the Malayan Tapir, Indian Rhino and Orang-utan. This area just seems to have been forgotten and I hope with the renovation of the orang exhibit, the other species aren't left out.
Older sections of the African pavilion, such as the Pygmy hippo exhibit
Outdoor Gorilla habitat
An unofficial add in, exhibits which I'm on the fence about:
Eurasia has some good enclosures but I'm really looking forward to its renovation.
Americas Pavilion; see above

The jag exhibit has its plusses and minuses but again, but I'm glad they're on the list of getting a new enclosures. Slightly off subject perhaps but I think this exhibit could still make a good exhibit for another smaller carnivore, such as Bush Dogs or ocelots, or maybe even Harpy Eagle with proper adjustments. A small herbivore such as Pudu might do okay here too.
Sumatran Tigers probably have one of the better exhibits in Indonesia, but could still do with improvements.
Snow Leopards; too small for the species but like the jaguar's exhibit, could still be a good exhibit another smaller carnivore. Red Panda if they're going to relocate them in the zoo, or Pallas' Cat?