I've been to both stores and they are pretty much the same. I haven't actualy bought anything or dealt with the genius bars however. The sales people were nice in both stores. I use the stores as a place to checkout the products in real life and then just buy them online and have them delivered. I would say just go to the one closest to you.
But as far as the malls themselves; Millenium is a a high priced, snooty mall. I much prefer going to the Florida mall. Plus that's the closest one for me.