Seems to be pretty much a slam-dunk for Vienna, or does anyone want to make a case for Plzen?
The main case I'd be making would be for the single point, and other than
@Giant Panda everyone is giving Plzen that one point
But to expand a little on my remarks above, which I meant to do sooner......
You are definitely right about some of these, but I definitely disagree on others
Callichthrid House
This one has been discussed a little previously - I get the impression you have a rather more sour impression of the whole South American complex than do most other people, but personally I think it's really not bad at all.
Madagascar House
I agree with you half-way, but only half-way

the indoor diurnal exhibits are indeed not great, but the outdoor exhibits and the nocturnal exhibits aren't bad at all.... and per my October 2019 visit, your accusations that some of the outdoor exhibits were going unused and thus exacerbating the indoor crowding were inaccurate.
Chimpanzee Housing
No arguments from me here
Philippine House
You highlighted the older portion of this house as a poor point for Plzen, but I'd strongly contest this - especially given the fact that this whole area has recently been refurbished both inside and outside, with some species moved to other areas of the zoo and the general decor being revamped. Moreover, the newer portion of this house, which you completely skated past, is excellent.
Pygmy Hippo Indoors
No arguments from me here either.
A mostly post-stamp reptile collection
Here, I definitely have to disagree with you on both the accusation, and the implied connotation; a large and excellent reptile collection (with island endemic species being a particular highlight) is something quite different from a "post-stamp" collection, and you know it

I have, of course, argued extensively in favour of Plzen in this regard previously.