I'm usually like Dragonite, designing each environment and then deciding what Pokemon would naturally fit there after (with bias for adding type variety and differing species). I find it's a really relaxed way of designing the dex but it's easy to lose track of what Pokemon are included. It's also fun to make
a spreadsheet, or use a tool like
Stardex to organize your region ahead of time. I'd say the main drawback of doing it in that order is just that...perfecting your dex balance is one of those tasks that can be endlessly revised, and stressing too much about it can get the whole project stuck in the pre-planning stages.
I reccommend trying different methods! You might assume that one way of doing things suits your personality, but the style and size of each project can really change your perspective.