Sorry for not replying on this thread, but thanks for all your advice!
I went last week, and decided to see the three main zoos: Planckendael, Pairi Daiza and Antwerp Zoo in three days (yes, it was busy but also very fun)
Went first to Planckendael, directly after arriving in Antwerp with train. It was a super hot day and very overcrowded in the park, so I didn't enjoy it as much as I thought I would. But a nice park with an interesting collection, I saw both wombat, echidna (first time seeing this species) and koala. Also their elephant and bonobo exhibits were outstanding! Savannah was ok, the rest of the zoo was alright, but nothing spectacular. I will return sometime, but not in a few years.
The next day I went to Pairi Daiza. Took an early train from Antwerp (6:30 in the morning) and arrived to the park about 30 minutes before opening. Also this day was extremely hot, but the park wasn't overcrowded which was nice. The exhibits were pretty good (some mediocre though, like the African elephant exhibit) and it was quite strange why the wombats and meerkats were in the Ganesha exhibit. Chinese garden with sleepy pandas and golden takins (didn't see those) was good, as were the Australian exhibit. Birds of Prey show was nice, the aquarium was pretty good but a little over-themed. I will definately come back, but will wait a year or two until the park is more finished (with wombats, snow leopards, Chinese giant salamanders etc)
Saw the Antwerp Zoo last day, went through the whole zoo in four hours (I had to pass my train to Paris in the afternoon). The zoo had a nice collection; Mountain gorilla, okapi, penguin house, reptile house, nocturama and bird house. I was looking for the kiwi exhibit, but I couldn't find it (are they still keeping them?). Overall it was a nice city zoo, but a lot of the exhibits were on the small side (birds of prey, tigers, leopards, monkeys).
Once again, thanks for your advice!