Usually, I create or adopt a very low quality character that has something I like or could develop. Then, I develop a story, and then personalize the design as the story evolves. I have several AUs and different designs for each character, but usually a good-looking, final, and consistent design comes out of it. The design usually ends up being moderate-simple in complexity for me, but it depends on the species, the world, your knowledge of the world, and your personal tastes.
There’s nothing wrong with starting with a character that resembles a cannon character or a Mary Sue. Search, research, and experiment, and find what you like. Then use things that seem to work together. A mess of a character with a complicated, random evolution is the most natural and human feeling character.
Basically, start with any character you like, ripped off (if can legally rip off... you can be sued for stealing from other artists, stick to tv shows and books or not), do a lot of redesigns with features that you like, and you’ll have a unique and pretty nice looking design.