Ugh, that situation in Store #1 hits so uncomfortably close to home with me that it is depressing. Not as in the McFamily taking over my gaming space, but in an uncomfortable familial situation that I am hesitant to go into too much detail for because of potential legal issues. But I can saw that I know a woman like the one you mentioned, who cares for a kid like you mentioned, and it is horrible when kids are allowed to be wild and uncontrollable in any situation because they have been "labeled" with something and their caregivers use that as an excuse to let them get away with anything. And in my dealings with it, it is depressing and heart-breaking, but I can't go into that.
Blech, anyways, I would have to generally agree with everyone here on recommendations:
FLGS #1 - Have a polite but strong conversation with the store manager/owner about the problem. Gather up the others who are bothered by this situation, and stand your ground as a group; if one person complains, it's no big deal, but if several stand together about the problem, that can elicit change.
FLGS #2 - I wouldn't go there anymore, ever again. The envirnment you have described is exactly why I stay out of big cities and like living in a semi-rural community within a couple hours drive of nearly a dozen individual gaming stores (though I only frequent 2).
Your
GW store manager needs to take a chill pill. My local
GW has had two managers: the first was a cool guy that didn't bother me too much since I spent enough money there that he didn't mind (
). The second manager was extremely pushy on product, to the point that I quit going for almost a year. I went back again later, and his tune has changed, and the secdon manager is much more relaxed and not near as pushy on returning customers as he was before.