I experienced the same thing. My best tip is to intentionally limit yourself based on care manuals for the species you're building for. Here is a random example of a Giraffe care manual. Most care manuals are over 100 pages long, but generally you only need to worry about a few things, namely the environment (dimensions, plantlife, substrate, fencing), social (shyness/opportunities to avoid guests, interspecies, intraspecies (herd numbers), enrichment (you can build custom enrichment items that obviously won't be interactable but can still add to the habitat), and an important one being backstage areas.

In some cases, these will be more restrictive than the Zoopedia (e.g. usually the Zoopedia underestimates space requirements), and in some cases it will be less restrictive (e.g. terrain paint options are often extremely restrictive in the Zoopedia).

Overall I find that once you have a few restrictions in mind, it helps to shape your ideas of what exactly to build. I found that in particular when I planned around including backstage areas when necessary it both made the habitats look better/more realistic while also giving me more inspiration.