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: 
Perhaps the problem you are having is you are thinking about it as "character development" not storytelling. Many writers start off working on their work with a formulaic engine of what is going to happen. They know where, when, who and why. They believe this will make their story compelling since they dot every "i" and cross every "t".

* If your characters move through your story as if they already know what is going to happen and are simply reacting to it, this removes the sense of tension you are looking for and thus they cannot "develop" or change.
* Yes, there are characters who are not changed as they move through the story. But in those stories, the environment changes completely around them. This usually means in the end of the story there is no place in the new world order for them. Think Rhett Butler in Gone with the Wind.
* Character development is what happens after something unexpected happens. If your characters are not experiencing the new, the different the unexpected and are not changing because of it, they are not developing and will remain flat as their responses to events is unchanging.
* It isn't enough to differentiate them by style of clothing or behaviors you write in with their descriptions. You have to find a way to make the reader feel them, want to know them, fear them, fear for them.
* This can only happen when you are willing to present them as fully as possible, revealing them the same way you would find if you peeled an onion. Yes, there is more onion beneath the first, but your goal is to describe the deeper layers of your characters. Just like with real people, what's on the surface is only the tiniest bit of their character. Their true desires, fears, ambitions, may stay completely hidden due to forces outside of their control, i.e. their religion, their family expectations, their social obligations, the nature of their desires, which may be considered potentially perverse or taboo in their society but not in others.

This is the tension you seek when you are looking for character development, the push-pull of the character toward his/her goal while dealing with opposing forces, inner motivations and the overall plot of the story which is what moves the character into opposition with his environment in the first place.
When I create characters, after creating their appearance and personality, I usually try to think like them. There are almost always some key attributes of a personality, so try being that person for a while. Just thinking like them is enough.

For instance, there was once one truly evil character. For a time I forced evil thoughts to the point when I was becoming evil. I had an evil character, knew how diabolical minds think (to a certain extent) and could appropriately write about him. [: