If you can only choose one of the two, I would choose Werribee Zoo: It has a nicer feel to it - larger enclosures, more space and a nicer natural environment. While a few people on this thread have mentioned the smaller number of species displayed at the zoo, this doesn't take into account the numerous WILD species which simply live within the grounds of the zoo:
At Werribee Zoo over the years I've seen platypus in the river (Werribee is one of the only zoos in the world with a river running through it), wild wallabies, wild birds such as pelicans, fairy wrens, cape barren geese, magpie geese, cockatoos, galahs, owls, numerous other birds, various reptiles including small lizards, as well as the odd snake, bats, possums and (introduced) rabbits.
A zoo with that much native wildlife within its grounds is certainly worth visiting - especially for someone not from Australia. There is also a natural wetlands on site, as well as a tribute to the old farm which was there before the zoo - including the old shearing shed etc.
As for the "zoo animals", they have large, naturalistic enclosures (no small enclosures or cages etc), and are displayed well.
The cafe is also good.
One caveat though: if you like/love snow leopards (as I do), then maybe Melbourne Zoo is the better choice - but if not for the snow leopards I'd choose Werribee every time.