Another brilliant section of the Zurich Zoo. Which of the Swiss zoos did you prefer on your recent trip? It is somewhat ironic that the worst part of each zoo is arguably the great ape enclosures.
Between Zurich and Basel, I'd give the edge to Zurich, though both are very strong. As you say, both are let down by the ape houses. Mulhouse Zoo (not Swiss but French, of course, but part of the trip) is a wonderful setting and great collection but has perhaps less 'wow factor' in its design. The director seemed very keen and I think it's a place that's only going to get better. The final place on the trip was Tierpark Lange Erlen (in Switzerland, just - it's in the north of Basel very close to the German border) - a very nice free-to-enter collection of mostly native species in a public park. I say mostly native, but the highlight there for us was the group of White-tailed Deer - very rare this side of the pond. I've requested a gallery for this place so will upload photos when I can.
On balance, I think the short answer to your question is Zurich. But they're all places I'd go back to, once I've got a few more new collections under my belt!