It can be VERY hard sometimes to wrap my head around characters. Of course, they need to be complex, or they read flat, which is what makes it so hard and what makes it so rewarding when you succeed. I'm afraid no amount of planning is going to build a three-dimensional character. What builds a well-rounded character is learning about them through the situations you put them in and how they react.
I have found that, often, one aspect is the key to a character. I was having trouble with one character, who seemed to be indistinct and was all over the place--was she an innocent ingenue, or a schemer? Then one word came to me ("pride"), and I was able to wrap her character around that core. How does she react to her mother being an obvious flirt always trying to sleep her way into a better situation? With disdain, because of her pride. How does she react when her lover publically announces his engagement to another woman? With anger and, again, disdain (for him). How does she get back on her feet? Pride.
In another case, I was having some trouble distinguishing two brothers, who were two of four POV characters. Both were troubled and depressive. As I wrote, I realized that they actually reacted differently: one reacted with fear and withdrawal, the other with defensiveness and sulkiness.
See, it's much more about the inner mechanisms of the mind than the surface manifestations (the particular likes and fears, etc). It's not all about the character's history, either; people with similar life stories end up very differently, after all. It's about how they deal with their own pasts and how it informs their reaction to the present, and how the present affects their future reactions.