Personally, I would hash out the issue in-character in almost the same terms as out of character. While the character wouldn't say things like "+9 stat points to HP and SP DEF", he would say something like, "Its amazing how the son is already clearly stronger than his mother. I'm so impressed-- but I don't want (insert momma's name here) to feel like she's being replaced."
Maybe even ask other PCs and NPCs for advice in-character. Then come to a decision that seems natural for your character or, perhaps, represents some sort of growth on his part.
With some good writing, you could probably make retiring the mother not seem icky in terms of good roleplaying.
[EDIT] I mean you still would have to be WAY worse to get anywhere near the level of pokemon retiring douch-bagness as Ash in the anime. That guy is a total ass to his pokemon.