Question: I'm 1/4 through my first novel, with a pretty solid 12 page outline of the whole thing. After years of reading books about story structure, I think I have a good grasp on how to make a plot work.

My characters, however, are turning out to be quite flat, uninteresting and generic. They do have motivations and I'm putting a lot of effort into making sure they act accordingly, in a logical way according to their goals and the story seen from their perspective, etc. But they don't feel "alive".

I've read about the archetypes in The Writer's Journey, but that's about it. How can I make my characters come to life?

Answer: 
Finish the book, then go back and look at the characters again.

When I start writing my characters are fairly generic, flat, and frankly cardboard. Character is my weakness, I love plots and ideas.
The crucial thing is that in the second draft, I then go back and add in bits of the colour, life and uniqueness which the characters have only accumulated by the last chapter.
Sometimes this will require changes to the plot (I'll realise that Rachel shouldn't have done that in Chapter 2, it doesn't fit with a part of her character I only realised in Chapter 7), but overall I find this a much more organic and natural process than trying to specify everything about a character before I know them, and as such the results tend to be much more convincing and compelling.

Your mileage may vary, but I think if you're a quarter of the way through without your characters having sparked yet, you're probably more similar to me in this respect than most!
Making realistic characters starts with knowing them. Pick your top few characters, and write a character bio. To write a bio, you must answer some questions about your characters. Here is a non-exhaustive list of a few questions to answer about your characters:

* Where were they born?
* What kind of family did they grow up in?
* What are their likes and dislikes?
* What do they look like?
* What are their core beliefs? (i.e. moral, religious, etc)
* What do they sound like (voice, dialect, etc)
* How do they interact with others?
* What type of people do they have as friends?
* What type of flaws do they have (everyone has them, and if your characters don't, they won't be believable.)
* What is their back-story?
* What culture did they grow up in?

Each question like this informs your characters, and provides a texture and richness.

Also, your main character should change through the course of the work. The typical method is giving your character a fatal flaw that he or she must overcome to achieve the goal of the story.