I've used the Atlas map generator mostly to create custom map sizes for scenarios--that to me is my favorite feature. I have also experimented with the map generation itself, & the only problem I'm finding is with regards of the river generation--they aren't made correctly, & unless I set the river density to really high levels, the amount of rivers is still not optimal.
Something I would do with this is create the map w/o rivers, & then add them via WorldBuilder, & to my liking. If you can take care of that detail, I'd be really satisfied with this.
@ Kanzera--this works for BtS, but if you want to select BtS-exclusive options, you can load the map as a 'Custom Scenario' & add them.