The tool-less riser card holder definitely feels more secure as well. It can be tough sometimes to get closed because the cards can shift out of place slightly, but once it's latched, it stays latched. And Apevia opted to include four of the 120mm fans with the X-Jupiter; two LED and two regular fans. The only spot left open is the top blowhole and depending on the size of your power supply you might not be able to mount a fan there anyway.
When it comes to looks the X-Jupiter and Junior share a similar style, but the X-Jupiter seems to be rubbing Jr's nose in the fact that it's really a nicer case. I'm reminded of the children's song that goes, "anything you can do, I can do better". Where the Jr. comes with one fan controller and two fans, the X-Jupiter has two controllers and four fans. The Jr. has two top mounted USB ports, whereas the X-Jupiter has two on top and two in the front. Where Jr. comes with a latch for you to provide your own lock, the X-Jupiter comes with two key locks already built in. To top it all off, the X-Jupiter has more room and weighs less, and bare aluminum looks so much better than painted steel.
If I could change anything I would ask for all four fans to be LED, rather than just the side and front. Also some openings behind the mesh front on the door panel would be nice. I mounted my iCage with fan in the 5¼" bays and airflow is limited with the door closed. There's also a little more restriction than I would like behind the front intake fan where it blows across the hard drive cage. But I am grasping at straws here, Apevia has a very good design with the X-Jupiter and even though I normally don't like full tower cases, the ability to remove the feet allows it to sit much lower, and doesn't have any issues fitting under my desk. In fact, I like the X-Jupiter so much, it's going to serve as my main case for awhile I think. I may have finally retired my old mid-tower.
At slightly over $150, the full size X-Jupiter will run you twice as much as the X-Jupiter Junior, but you definitely get your money's worth. If budget or space constraints are top on your list, and you like the X-Jupiter style, then the Jr. may be the one you settle for. But the X-Jupiter is the one you really want.