I'm not sure how flying creatures could be made fun, but aquatic creatures opens up a whole new realm of underwater facilities, viewing, transports, etc. Just because it's underwater doesn't mean we can't get down there or provide guests with ways to view the creatures. Dangers that need to be managed could be the vulnerability of any underwater transports or glass-bottomed boats, flooding of underwater facilities, etc. I can totally see a lot of fun systems built up around this.
Flying creatures... I'm really not sure. Build an aviary... done. Meh.
Flying creatures... I'm really not sure. Build an aviary... done. Meh.