#1 1.1, 1.2, etc. is never being sold in stores. Maybe 2.0 with all the extra creature packages for $45 will be sold in stores depending on demand for 1.0.
#2 You can buy the jewel-case only version of the Aquarium for $14.99.
#3 I love the big box, even if it's a waste of shipping space. It's a huge box and just the jewel case inside. I've got the box standing up at the corner of my desk where I intend to keep it for some time.