That's what on top of my head too - Avilon Zoo than Manila Zoo. I'm a Manileña since birth and I used to love Manila Zoo when I was a kid. But the last time we visited it (I think in 2013) I got so frustrated as it's no longer pleasing. So I won't recommend it anymore. For some reasons, I think it's time the city government need to look into this and perhaps do something about the management. So yea, go visit other zoo. You can also try Birds International in Fairview QC or Zoobic Safari.
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I'd suggest Avilon Zoo in Montalban, Rizal. Nicer surroundings, less people, gorgeous animals. They also have a petting zoo in the Tiendesitas area if you want to stay within the city first.