I have been wanting to switch from FasTrack to Atlas-O, but am dissuaded by the hassle and cost of Atlas-O (wiring and ballasting). The deciding factor I always come down to is the command control switches with integrated switch machine. I don't have to run power or control wires, everything is through the rails. I like easy!
But I like the looks of Atlas-O, and flextrack and numbered turnouts are great. Lionel should add #4 turnouts to FasTrack, IMO.