There's certainly plenty of rare and unusual species within those collections - to name but a few, Southern Aardwolf and Thick-tailed Galago at Dvur Kralove, Javan Ferret-badger at Brno, Transcaspian Urial at Chomutov, Afghan Uriel and East Caucasus Tur at Liberec, and Coyote at Olomouc.
As far as exhibits go, probably the most notable/significant are the massive safari reserve at Dvur Kralove, the gallery of Czech palaeoart at the same collection, and the mixed exhibit for bears and langurs at Ostrava.
It's pretty much a full-day zoo and public transport from Prague to the city of Zlin takes a long time and several transfers, with the zoo itself being several miles outside the city. Much easier to reach the zoo from Vienna all things considered.