I don't think Streep's qualifications to play the role would ever be in question. Nor is a comparison between Cherry Jones and Meryl Streep's interpretations quite fair. Film, by virtue of close-ups and editing, can do things that theatre can't, and by comparison, the electricity of live theatre when it is at its best, is a sensation I do not usually experience even at the finest movies.
If I had to compare the performances, I'd say this: for me, Cherry's Aloysius seemed absolutely resolute in her conviction until the play's final scene. Streep seems to allow some consternation and vulnerability creep in starting with her scene with Viola Davis. Both Aloysius performances are equally forceful, terrifying and imposing - and funny.
As for other questions about Shanley's work as director, I don't think it is my place to "grade" his efforts (I leave that nonsense to pop culture magazines), but it is simple, unfussy, generally clean and direct, without calling attention to itself. Since Shanley grew up in the Bronx at the time Doubt is set, he also knows the neighborhood and the look of the film feels right in its production design and attention to detail.
Regarding the other characters that were in an early screenplay, apart from a few shots of William London (the one who "would set his foot on fire" for a day out of school) and a boy who is sent to see Aloysius after talking out in class, there is no material in the cut I saw examining the "mental growth" of the other boys.
Begin at the beginning and go on till you come to the end: then stop.