I use to be a big earth 2 guy, but now I feel that putting them on a different earth has really lessened the characters' prominence. Look at Powergirl for example. Back when she was on the primary earth she was everywhere, but now that she has been relegated to earth 2 she barely shows up in anything, that isn't cosmic in nature. I feel that is the problem with the JSA being on earth 2. Most of the action( stories) takes place on earth 1 and inorder to involve earth 2 characters you have to make the story an interdimensional adventure of cosmic importance. That works for some types of stories (big crossovers), but it becomes hard to justify with most other types of stories. So you have a situation, where you took a bunch of interesting characters, and shoved them into a place where they can only interacted with your major characters in big crossovers, or in contrived situations, where the author really has to work hard to justify the need to cross dimensions.
Some people hate the 90's JSA, but you could never say they were shuttled off into irrelevance like the modern one has been. They were pretty effectively weaved into the DCU tapestry (especially during the John's run.) And some pretty important arches and runs spun off from them.(Starman for example). Plus I felt it was the place where the legacy element of the DCU was most prominent. The JLA was the face of the DCU, but I felt the JSA was kind of the heart. Plus JSA/JLA crossovers are more interesting when you have those quasi-family bonds between the two groups.