I don't know. I feel like there are only two ways that could go:
Not making her a gym leader at all: I've always seen the Trainer leaving home and going on an adventure as a sort of rite of passage, going out to make a name for themselves and achieve glory. Having Mom help you out when you're well along your journey and should know what you're doing, and having to fight her for a badge, just doesn't mesh all that well: It would kind of take away from my view of the Trainer's journey.
On the other end of the spectrum, make her the Champion: Have her be this legendary trainer who conquered the best of the best, and everyone's looking forward to seeing what you're capable of as her kid. Have her not just coach you at certain points, but pummel your rival's team on occasion, give you items to proceed, help you fight the Team of the region, and generally make her out to be the most bada** of bada**es. That way, when you face her after fighting the Elite 4 and beat her, you're finally out from under her shadow, the new generation has beaten the old, and you have solidified your reputation as the best like no one ever was.
All this 100% it'd be a hell of a twist
The voices in my head may not be real, but they have some good ideas! <(^_^<)(>^_^)> Official Yarne of the FE: Awakening Board! Bunny monster!!!