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I'm not sure that I see her character as 'not adding up.' Rather, as I mentioned RE James in my other comments here, people can show different facets of their personalities/behave differently with different people and in different situations. Severus and Harry stand in totally different relationships to her, so I don't expect that she is necessarily going to behave in precisely the same ways with each. Also, unfortunately, people don't love other people all to the same degree, for various reasons. I can totally buy that she is more deeply attached to and caring of her own child than she is of the kid she was (from her POV as I read her) sort-of-friends with during the summers her first few years at school and who insulted her.
The "saintly mother" image IMO is just that: an image, manufactured after her death and by the author (although Harry IMHO never seems to fully grasp that it is an image, nothing more, but then his only real experience of her that he remembers is in images of her, actual and narrated. People don't like to speak ill of the dead, especially not the heroic dead, and to their children). It's not that we see many scenes of Lily being the perfect mother: we have one brief letter of hers from the time and one scene of her in a highly unusual circumstance, trying to save her own baby, which I think any mother with a modicum of caring would do. It's one thing to die for one's own child; dying for (for example) a stranger's child, or a child you despise (no you oughtn't to despise them), etc. is another kind of challenge. Both are brave and admirable, but one requires a greater extension of unconditional love than the other, and is correspondingly more difficult. The one marks her as a genuinely loving mother who is brave; the other would mark her more as a saint. IMHO. In her letter, she comes off to me as a sincerely loving and good mother but also a young and slightly irresponsible parent who is just starting to get the hang of the parenting thing (unsurprising, since she is just out of her teenage years).
He relationship to James also actually doesn't come across as so OOC to me. Lily seems to me to be the sort of person who, while meaning well, likes to get on a moral high horse and be the voice of morality instructing all around her in her wisdom, regardless of how much wisdom is really there. (Certainly she genuinely believes she knows best.) In this James is just one more 'student,' like Severus, except he's one (she thinks) she's actually gotten through to! Clearly there's something to the fellow, she thinks. Also, while she likes the image of moral saintliness and thinks well of herself in that regard, she comes across to me as slightly more shallow than she cares to admit (hardly a surprise in a teenager, and a common temptation for everybody, I suspect). She does care about her social image, and though calling her a golddigger IMO goes too far, I could find the prospect of wealth as one among several threads of her *initial* attraction to James believable, given how much her sister cares about such things (meaning is strikes me as something stemming from their childhood together). Later something genuine could have sprung up between them, I can buy that. She and James are not that far apart in basic personality, although she doesn't possess the same streak of sadism as he does - but he hides that from her. She also is fiery and rather Gryffindorish, so she and James are rather well-matched there in personality; she can be somewhat cold, though not necessarily deliberately; empathy is not beyond her but also comes to her naturally only to a limited degree, and Gryffindor isn't a house that really teaches one to value or expand it in practice. (The rhetoric is another matter.)
The "saintly mother" image IMO is just that: an image, manufactured after her death and by the author (although Harry IMHO never seems to fully grasp that it is an image, nothing more, but then his only real experience of her that he remembers is in images of her, actual and narrated. People don't like to speak ill of the dead, especially not the heroic dead, and to their children). It's not that we see many scenes of Lily being the perfect mother: we have one brief letter of hers from the time and one scene of her in a highly unusual circumstance, trying to save her own baby, which I think any mother with a modicum of caring would do. It's one thing to die for one's own child; dying for (for example) a stranger's child, or a child you despise (no you oughtn't to despise them), etc. is another kind of challenge. Both are brave and admirable, but one requires a greater extension of unconditional love than the other, and is correspondingly more difficult. The one marks her as a genuinely loving mother who is brave; the other would mark her more as a saint. IMHO. In her letter, she comes off to me as a sincerely loving and good mother but also a young and slightly irresponsible parent who is just starting to get the hang of the parenting thing (unsurprising, since she is just out of her teenage years).
He relationship to James also actually doesn't come across as so OOC to me. Lily seems to me to be the sort of person who, while meaning well, likes to get on a moral high horse and be the voice of morality instructing all around her in her wisdom, regardless of how much wisdom is really there. (Certainly she genuinely believes she knows best.) In this James is just one more 'student,' like Severus, except he's one (she thinks) she's actually gotten through to! Clearly there's something to the fellow, she thinks. Also, while she likes the image of moral saintliness and thinks well of herself in that regard, she comes across to me as slightly more shallow than she cares to admit (hardly a surprise in a teenager, and a common temptation for everybody, I suspect). She does care about her social image, and though calling her a golddigger IMO goes too far, I could find the prospect of wealth as one among several threads of her *initial* attraction to James believable, given how much her sister cares about such things (meaning is strikes me as something stemming from their childhood together). Later something genuine could have sprung up between them, I can buy that. She and James are not that far apart in basic personality, although she doesn't possess the same streak of sadism as he does - but he hides that from her. She also is fiery and rather Gryffindorish, so she and James are rather well-matched there in personality; she can be somewhat cold, though not necessarily deliberately; empathy is not beyond her but also comes to her naturally only to a limited degree, and Gryffindor isn't a house that really teaches one to value or expand it in practice. (The rhetoric is another matter.)