I'm of the opinion that your characters are more likely to be flat if you DON'T base them on some deeper human thread.
Theme is what makes character-driven work actually hold the reader's interest. Granted, theme should be subtle, if not invisible, or you'll prevent the reader from making the story his own. But if it's not there, why should he care?
No character is interesting enough to hold a story together, unless that character is involved in some kind of conflict that is rooted in complex human behavior. And the theory behind that behavior is theme.
You CAN get theme from character, or character from theme, or theme and character from setting. But whatever way you approach it, a well constructed theme is never a bad idea.