FTBlauncher is better IMO. Some of the Packs on the ATlauncher require you to download from other sites which increases the chance of infections.
Now before I say this, I like both Launchers Mainly because there are packs on both that I play.
The ATLauncher uses 9 Severs for pack downloads, and FTB has 10. I'm not sure what your talking about other sites? If you mean that it opens a window "Some times" while installing a pack, that would be a mod that has no modpack permissions, but can be used if you get it from the mod creator. This is a good feature, because it points you to a mod without having to hunt for it. Again, like both, just saying.