This is the most famous game involving animals in Tokyo. It features a unique "relationship" system:

I need to verify if there are any specific works, authors, or directors that use Tokyo zoos in their love stories. Maybe searching for Japanese media that features Ueno Zoo. For example, the 2010 film "Tokyo Tower" doesn't involve a zoo, but maybe another film does. Alternatively, the 2011 anime "Nausicaä of the Valley of the Wind" has elements of nature, but that's more fantastical.

Some popular Japanese media featuring romantic storylines include:

: Located in Ueno Park, it is the most famous romantic spot. The storyline for a real-life couple usually includes a walk around Shinobazu Pond