I had trouble with Meggie as a protagonist. She was such a ... milquetoast/doormat/milksop (trying to come up with best word).
On re-reading, there's something about Father Ralph which annoyed me. Throughout the book, we're told how intelligent and perceptive he is.
When he sees Meggie's son, though, it never once occurs to him to think, "Hmm. I once had a lot of unprotected sex with this young woman who's been in love with me forever and who wanted children desperately. Now she has a son with blue eyes (like me), who's a polyglot (like me) and who wants to be a priest (like me). I wonder..."
No, this paragon of perspicacity doesn't even ask her who her son's father is, or when her son's birthday is, so he can do the math. Instead, he leaps to the conclusion that after their romantic interlude, she went back to her husband and had
his child, although there's no reason at all why she should have done this (and she's already told him that she had to "scheme" to get her husband to knock her up the first time, so there's no reason why the husband would cooperate for the second child). To everyone around him, the truth couldn't be more obvious, but he persists in his blindness until the end. Talk about sacrificing character consistency for drama.