I expected this to be an easy win for Berlin, and I did vote for it, but while typing this post I realized the great bird exhibits are actually quite even...
Birds:
Berlin, of course, has the two excellent bird houses. Both have enormous collections in aesthetically pleasing buildings and outdoor aviaries. The African walkthrough in the center of the new bird house felt a bit bare, but the very lush Asian walkthrough next to it made up for that. I've not seen the kiwi enclosure, but apparently it is decently designed and the animals are often active.
Besides that are a very large walkthrough aviary for waterbirds and a giant aviary for condors, both very good for the animals and definitely interesting exhibits. The lakes throughout the zoo hold very many waterfowl species and large group(s?) of flamingos and pelicans. Other things like the penguin house, shore aviary, and large ground birds mixed in with hoofstock or in single exhibits (rhea, ostrich, ground hornbill, crane, stork), along with the very recently renovated area for birds of prey definitely make this a very good zoo to visit when you want to see birds.
Bird highlights in Berlin are (and are definitely not limited to) Andean flamingo, James's flamingo, trumpet manucode, Northern brown kiwi, kagu, golden-headed manakin, spangled cotinga, purple roller, Arctic tern, Australian pelican, long-tailed fiscal, channel-billed cuckoo, white-browed coucal, copper sunbird, greater yellownape woodpecker, white-eared catbird, Indian pond heron, pale-billed aracari, pied hornbill, palmnut vulture, Visayan tarictic hornbill, and many more.
Prague doesn't have a bird house yet, because it's still being built. I think upon completion this challenge might have gone differently, but as of now it's hard to say. I'd say Prague's best bird enclosure is the Sichuan house, which is actually quite comparable to Berlin's bird house's Asian walkthrough, but with a completely different atmosphere and more interesting species.
The shoebill exhibit, surrounding crane exhibits and waterbird aviaries are definitely very well designed, and I think a setup like this works better than just having a lot of species in a lake (like Berlin's ducks) or a lot of species in a huge aviary (like Berlin's other waterbirds).
Prague also has a giant vulture aviary, and I'd say Prague's definitely beats Berlin's condor aviary because Prague's is built against a giant cliff face. However, Prague's other birds of prey are housed in fairly unimaginative cages on the edge of the zoo, not quite as nice as Berlin's bird of prey area (which I haven't seen since the renovation, but I have seen a few pictures). Other bird enclosures are dotted around the zoo, for ravens, owls, ibises, lammergeiers, flamingoes, pelicans, penguins, and a few rows of nice but unimaginative aviaries for African and Asian passerines and hornbills, which work well in summer but are all but empty in winter...
Exhibits that do stand out are a duo of good spacious walk-in aviaries for European waterfowl, a few very nice small aviaries for European forest birds, the Indonesian pavilion (probably great for birds, but not for visitors trying to see birds), and an excellent row of lorikeet aviaries overlooking the entire zoo.
Bird highlights in Prague are (and are definitely not limited to) chestnut-bellied sandgrouse, four-banded sandgrouse, shoebill, coleto, Edward's fig parrot, silver-eared mesia, greater yellownape woodpecker, Gray's piping-guan, helmeted friarbird, horned lark, large fig parrot, lesser yellow-headed vulture, Peruvian thick-knee, metallic pigeon, spot-billed pelican, Sunda whistling thrush, vernal hanging-parrot, Visayan tarictic hornbill, Luzon hornbill, Siberian rubythroat, silver-eared mesia, hooded pitta and many more.
Off-show species that will hopefully make it into the new bird house are green magpie, Javan green magpie, Lear's macaw, green oropendola and New Guinea bronzewing (though those last ones are already visible from the path, if one knows where to look).
In general I prefer Berlin in this match-up (the fact that they have a bird-of-paradise and a cotinga may or may not contribute to this), but it's a close one... Berlin has the two very nice bird houses which have most of the collection, whereas Prague's collection is a lot more spread out in very different enclosures.
Carnivores:
This will be less in-depth than the text wall for birds above, but this is definitely also important. I think I'm slightly in favour of Prague, but I think Berlin's better bird collection makes up for that.
I prefer Prague's carnivore house over Berlin's. Architecturally to me it's just a lot more pleasing, and the consistent clean style in my opinion works better than Berlin's cages. Lions and tigers (if the tigers are still present? They're not on zootierliste... Does something else live there now?) are better off in Berlin's carnivore house though, with spacious and well-planted outdoor exhibits. However, all other cats get the upper hand in Prague, where they have more organic and lush aviaries than in Berlin.
For bears it's better to go to Berlin as they have a lot more species, all in decent to good enclosures, whereas Prague's polar bear exhibit is probably the worst carnivore enclosure in the zoo. Berlin's sloth bear and giant panda enclosures are good, the other species (Asian black bear and polar bear) are in grottoes, but quite spacious ones.
Prague does get outdoor enclosures for large carnivores right though, as is definitely visible in the great outdoor exhibits for Amur leopard and Siberian tiger. The enclosure for brown hyenas is also good.
The main pinniped enclosures are quite comparable I'd say, but Berlin has a few other enclosures and species as well, whereas Prague only has the fur seals.
In small carnivores (including smaller cats and canids) I think Prague has the upper hand, as I'm quite sure they have more species of a larger diversity.
Prague has brown hyenas, so it wins against Berlin for hyenas as Berlin doesn't have any.
For me, I think it comes down to this:
Big cats: Berlin = Prague (Berlin better for lions, Prague better for tigers and spotted cats)
Small cats: Berlin = Prague (4 species compared to 5, none really stick out)
Canids: Berlin < Prague (3 species compared to 6, wolves better at Prague)
Small carnivores: Berlin < Prague (8 species compared to 15, otters and mongooses better at Prague, though Berlin's two Malagasy carnivores do make this a bit tougher)
Hyenas: Berlin < Prague
Pinnipeds: Berlin > Prague
Bears: Berlin > Prague
I wonder how Prague's future projects for giant panda and polar bear will change this match-up!
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Phew, that took long to type! Sorry if I made any mistakes
