I don't think a bride is under any obligation to have children from her husbands family in her bridal party - and, indeed, I actually think the opposite is true.
So yabu.
I understand your mum feeling left out but think she should have limited her expectations, typically it's the brides mum who is more involved unless bride & MIL have a close relationship. So, again unreasonable but am sympathetic.
On the other hand, I think your brother & future sil are unreasonable to exclude your children in this fashion...
All this makes me think the wedding is a flash point for other issues, namely, that perhaps you & your mum feel like you're losing your brother to his fiance and that she is, perhaps, distancing themselves as a couple from your family.
In which case, getting upset & kicking up a fuss about flower girls isn't going to make a huge difference - it'll just drive a wedge between you and your SIL. You & your mother should focus on building your relationship (respectfully) with her instead and hopefully your brother will put a little effort into including his family into family gatherings (if he wishes).