It really depends on the type of zoo I want to build - a general zoo with no real theme overall, a location based zoo, a biome based zoo, or something else entirely. Knowing my maximum habitats are going to only be about 40 habitats, I know where i"m going with that when I start. If it's a general zoo I have an idea if I want to keep it large or small.
Location wise, I think this speaks much for itself. I keep to animals within that continent, with three exceptions - Giant Pandas, Meerkats and Koalas are allowed in any location based zoo. I just make them a part of an "Around The World" section to give a little bit of variety. Otherwise these do tend to be smaller type of zoos -I often shy away from too many high costing animals due to that limitation, though there's always going to be a couple in there somewhere.
Biome themed zoos are something I've gotten more involved with lately. I have three, a Tropical/Aquatic themed one, a Grassland themed one and a Temperate themed one, though I didn't realize it on that last one until recently. I've been using it as more of a campground type of zoo with common animals from around the world. But I realize now, overwhelming these are temperate animals. I do plan to or have incorporated animals from other biomes, but there's definitely a theme for a good portion of them. Noting I've not really challenged myself on the tundra biome, and I end up being a bit more selective in a desert biome because some of those animals just won't take that as well as warm natured animals being in colder environments.
General zoos are the easiest and hardest. Easiest because all options are available, hard because that gives you a lot of choices. I've tended to start with Meerkats, Red Pandas, Aardvarks, Warthogs, Timber Wolves, Koalas, Kangaroos, Clouded Leopard, and Giant Pandas as my first most likely group I'm going to be starting off with, in general. Adding to that the Badger as well I think. Giant Pandas are expensive on the market but not that expensive in upkeep and their appeal is huge. Only once I making good money with my first dozen or so species do I look towards adding in elephants, Tigers, Lions or Giraffes - with that last one sometimes sneaking in earlier than that. I don't know why but I tend to hold off putting Primates in for the most part until the zoo's extremely well established. Ultimately my goal on these zoos is get to the point I have at least six of the big 10 that the general population loves - a species of hippo, giraffe, tiger, lion, rhino, elephant, giant panda, gorilla, orangutan, and chimpanzee. These aren't even all in my favorites, though most are, this is more of just what I think the big animals in zoos are known for if they have them. Of all of those, I wouldn't even think to put 8 or 9 of those in my first 10 habitats, the giant panda and sometimes giraffe being the exceptions. Those are "long range goal" animals if you will.
Some other type of theme, that's where a real interesting focus can come in I feel. It leaves you thinking outside the box at times and the mixture of animals that end up in those varies. I have one zoo that's a small "cute" animal zoo, so outside of Giant Pandas and Snow Leopards, there's not going to be any really large animals.
And that's all just in franchise. In sandbox you can do a lot more ideas with options toggled off and not having to worry about money or welfare if you don't want to. I haven't done it yet but thinking about an Apex Predator/Prey type of zoo - in separate habitats, but near one another to give an educational idea of how the real life environment works. And of course, zoos that just have my favorite animals in them; you don't need to worry about costs and you can have any animals you want right away.
edit: TL; DR - theme of the zoo is important. If you know what type of zoo you're planning, you probably already have an idea of a handful of animals you want to see in it. Sometimes zoos outgrow their theme, but that's only if you don't limit yourself.
