I would also just say that I have visited Plzen and not Rotterdam (yet). I think Plzen has very good enclosures, and comparing the collections I find it appeals more to my taste.
I'm happy to consider a switch if someone makes a case that Rotterdam is actually better in some measureable way. At the moment I'm not sure why it is so far ahead, and I fear it's because people are applying the rule of thumb that Plzen's good collection is marred by small enclosures, which is not the case for ungulates.
I don't think Rotterdam is far ahead of Plzen, but I prefer Rotterdam over Plzen
I think your calculations are slightly off......
PLZEN: 27 TAXA
Domestic: 5
Bos primigenius f. taurus
Camelus ferus f. bactrianus
Capra aegagrus f. hircus
Equus ferus f. caballus
Ovis orientalis f. aries
Elephant: 0
Even-toed: 18
Antilope cervicapra
Bison bonasus
Cervus canadensis nannodes
Choeropsis liberiensis liberiensis
Damaliscus pygargus phillipsi
Giraffa camelopardalis rothschildi
Kobus leche kafuensis
Muntiacus reevesi reevesi
Naemorhedus griseus arnouxianus
Ovibos moschatus moschatus
Ovis canadensis californiana
Ovis dalli dalli
Pecari tajacu
Phacochoerus africanus africanus
Rusa timorensis
Tragelaphus angasii
Tragelaphus strepsiceros
Vicugna vicugna
Odd-toed: 4
Equus hemionus kulan
Equus kiang holdereri
Equus quagga chapmani
Rhinoceros unicornis
ROTTERDAM: 24 TAXA
Domestic: 1
Camelus ferus f. bactrianus
Elephant: 1
Elephas maximus
Even-toed: 18
Antilope cervicapra
Bison bison bison
Bos javanicus javanicus
Choeropsis liberiensis liberiensis
Elaphodus cephalophus michianus
Giraffa camelopardalis reticulata
Nanger dama mhorr
Okapia johnstoni
Potamochoerus porcus
Pudu puda
Rangifer tarandus fennicus
Rusa alfredi
Sus cebifrons negrinus
Syncerus caffer nanus
Tragelaphus eurycerus isaaci
Tragelaphus strepsiceros
Tragulus nigricans
Vicugna vicugna
Odd-toed: 4
Diceros bicornis michaeli
Equus quagga chapmani
Rhinoceros unicornis
Tapirus indicus
So in point of fact, Plzen has more hoofstock taxa than does Rotterdam - this being primarily due to the sizeable and very pleasant collection of rare domestic breeds displayed near the top of the zoo.
Both our scores are not wrong and neither is necessarily better, in the majority of this contest domestics have however not been included, which is why I left them out. People can decide for themselves whether they want to count them.
Just to get back to Plzen before I will give an overview of Rotterdam. I am aware of the huge water space the Pygmy hippo have, but indoors really is quite bad and as they are a solitary species I wonder how much time each Hippo can spend time in the large outdoor enclosure, the smaller side enclosure was not much to write home about...
Plzens hooftstock enclosures are mostly pleasant and spacious, but to me not particularly memorable, whereas in Rotterdam I would say there are currently 3 particularly memorable complexes:
1) The Giraffe house is visually stunning as well as spacious inside and the outdoors is also well done, quite possibly my favourite giraffe house (after the one in Berlin) The Reticulated giraffe share it with Greater kudu:
2) The Okapi aviary. It is not Doue and I have been critical of it, as it has replaced a fantastic native bird aviary and is not huge outside. The indoor part for the Okapi is easily the best in Europe and outdoors might not be large, but it is not smaller than in e.g. Basel or Frankfurt. The combination of Okapi with a large number of African birds works quite well and it livens up the enclosure:
This picture shows less than half of the total indoor space
3: Often overlooked in Rotterdam is the unique architecture of the place, The whole zoo was originally designed by one architect: Sybold van Ravensteijn and his work is quite unique and Diergaarde Blijdorp may be the best place to see his remaining work. The renovation of the former Elephant and hippo enclosures for Black rhino and Pygmy hippo is from an architectural point of view a triumph, if not somewhat small for the animals:
One of 3 Rhino outdoor enclosures
Rhino indoors
Soon there will be more hoofstock in Ravensteijn's architecture as pure subspecies Barbary sheep should arrive soon from Spain to share the wonderful Gelada enclosure:
The Elephant house Taman Indah used to be a highlight of the zoo and 25 years ago it was one of the pioneers in a new way of keeping Elephants indoors by moving away from small cubicles. Now it will be in need of renovation soon as space requirements have changed, but it is still not bad:
The same complex has also fine enclosures for Indian rhino and Malayan tapir, though the indoor situation is not optimal
(shows about half)
Some other enclosures spread around the zoo:
Banteng & Blackbuck
One of two Tufted deer enclosures
Visayan spotted deer
Bongo enclosure
Forest buffalo enclosure (which can be accessed by Red river hog as well
All in all Plzen might have larger enclosures, none really stick to the mind for me, whereas Blijdorp has several quite impressive enclosures. The focus might be more on architecture, but the Berlin Zoo would also be just an average zoo if not for the larger number of wonderful old buildings, which give the zoo a certain atmosphere. This match is close, but I would rather visit Blijdorp for its ungulates than I would visit Plzen for the same reason.