Characters
I usually start with a character and they are usually a Mary Sue and then I bring them back. My other characters are based on observations and wish fulfillment. Writing Excuses has done some really good podcasts on characters.
Diverse Characters
I think I might beg here. Please don't write characters that are rich white dudes. Their story has been told. So if you want to be original do your research and look at other cultures. The women don't have to be secretly beautiful or the men macho. Give other people a voice. Buzzfeed has an article on it.
Gary Sues and Mary Sues
Like I said before, I usually start with a Mary Sue. I then start giving them layers and putting them into situations that even being a Mary Sue they can't solve and like uncovering a Michelangelo sculpture the character is finally revealed.
You can find some really good templates on Writers helping writers, and not just for creating characters for many aspects of the creative process.
How to avoid the cardboard cut out
As a discovery writer I don't do profiles, instead, I write a scene. I'll know if they are real or not if their voice emerges. Helpfully as I write more books, I often can spin off other books from side characters from other books. But if the character doesn't have a voice, I struggle to figure out what they are going to do in any particular situation. Novel Now has some good pointers on this. If you are writing someone very much unlike you or from a different background, the magic bullet is research. Find out what your character is really like by talking to or researching people just like them. The Writer's Digest has some good tips.
Quirks, flaws, and Flanderization
Your characters should have flaws. If you don't know why please go and watch the clip on Mary Sues again. If you have no idea what flaw they should have here is a useful list from Writers Write. But if you have your character doing something just because you want them to be different from everyone else you are talking about a quirk instead of a flaw. Writer's Digest has a nice article on how to tell when you have strayed into quirk territory.
Your homework is to develop a character. Research them and make a profile of some sort and then write a scene where they are somewhere doing something.