I think the biggest sin of Japanese zoos is, above all, that they're transferred one of the most obvious details of Japanese culture, which is that everything is small: the cars, the houses… and therefore the zoo exhibits. In Ueno, for example, I've seen rhinos in enclosures that in Europe would be used, at most, for wild boars, or seals in aquariums where we would not even put otters... This is shocking and in some cases sad. But I must say that I have not seen sick animals in Japanese zoos and in general they look in good conditions. I think that the handling techniques, feeding and so on are good and I hope that the aspect regarding space will change little by little.
If you have visited zoos in Europe, Ueno could be an equivalent to any decent European zoo. Inokashira in general seems older, it is more outdated, with quite a lot of fencing, but it is'nt disastrous.