In James Joyce’s anthology, The Dubliners (specifically, ‘The Sisters’) what was the message of the story, and what ideas were conveyed?

"The Sisters," by James Joyce, is the first story in the
Dubliners.  It is also one of the most difficult stories.  It seems
incomplete.  There is much we, the readers, do not know.  But you can look at the story
in three different ways:

(a) the effects of adults on a
child:  The narrator is the lone child in a world of adults.  His relationship with
Father Flynn, while intellectually stimulating, is uncomfortable.  He learns much about
the church from the priest, but the boy is repulsed by Father Flynn's physical
deterioriation and emotional instability.  It is possible that the priest may have
molested the boy, especially in light of the short story that follows "An Enounter." 
Since the narrator is a child with limited understanding, we do not know the extent or
the true nature of the priest's influence on the narrator.  The other adults influence
the boy as well.  The sisters' exhibit the confining routines that paralyze many of the
characters in the Dubliners.  

(b) loss of innocence:  This
is the narrator's first experience with the death of someone he knows.  The narrator's
reactions, however, are not what he expected them to be.  Instead of mourning, he feels
a sense of relief.  When he visits the corpse, he does not see the "beautiful corpse,"
that the sisters describe.  Instead, he sees the "furry nostrils" and other signs of
physical decay. 

(c) desire for escape:  Father Flynn
obviously felt uncomfortable in his role as priest.  His lessons to the boy are those
that question the finer points of the church's doctrine.  He was a "conflicted man,"
according to the sisters.  His decline began when he dropped the holy chalice and made
public when he was found laughing in the confessional.  The boy, too, longed for an
escape from his daily routines and has a sense of freedom when he realizes that priest
has died.