I agree that this is hugely disappointing especially the fact that this was perhaps the best Clouded Leopard exhibit in the US.
The "zoogeography" of Monkey Trails was always pretty hard to discern: African monkeys viewed from the raised boardwalk with Asian pigs on the ground below them etc. The Clouded leopards are a loss--one of the few exhibits I've seen where they were frequently visible but in a diverse and naturalistic space.
In general, zoogeography or any other thematic organizing principle for a collection is only as good as an institution's management's dedication to following through on it. Never a strong suit at San Diego.