How is Scout Finch different from Lily Owens from To Kill a Mockingbird and The Secret Life of Bees?I know that one of the obvious difference is...

Starting with your idea of their fathers
- think beyond just the relationship each girl has with her father. 
Think about the relationship each girl has with her family*. 
Scout's is decidedly better, more loving, closer, and more
accepting.

* I think you could also make a pretty extensive
list of personality differences as a result of the girls' family situations.  They are
exactly as obvious as you would think.

Also, they have a
pretty distinct age difference.  Scout is just starting the
1st grade - Lily is 13 or 14 when the story opens.  *This is an ironic difference as the
perspectives sound as if the girls could be peers.

There is
also a difference in the education of each girl.  Both
receive an education as a result of experience, but Scout's education is decidedly more
formal.  It is influenced by reading, academic discussion, and being surrounded by
educated adults.  Lily on the other hand is clearly experiencing a new kind of education
- but hers is more of a hands-on, rural experience.  The time she spends at August's
house is valuable in a different way than books and academic discussion.  She is
experiencing a new way of living, directly.  This cannot be ignored as part of her
education.

There is a difference in the
time-period of each book as well. 
Mockingbird is set in the time of the great depression.  Sure, no
slavery - but this is during the time of accute segregation, Jim Crow laws, and a major
lack of racial equality as a way of life.  Lily lives in the 1960s - right in the heart
of the Civil Rights Movement.  While racial tensions are still high and equality is
still relatively low - the racism Lily experiences is more controversial on a global
level.  Whereas the majority of Scout's world doesn't even consider "racism" to be wrong
yet - Lily lives in a time when this debate was raging, Black America was gaining a
voice of its own, and there was the beginning of support from whites for this
advancement.  To put it simply, Atticus Finch would not have been in such a minority had
had his story been set in the 60s.