I also don't know if the CRS/GDS problem is indeed a big obstacle for joining an alliance.
When All Nippon (NH) joined Star a few years ago, their system was hardly integrated with other Star carriers in the first year at least. I remember I was surprised when they once told that they need 24 hours to confirm a booking for a NH coded flight operated by UA. (This problem has been 'redressed.' Star has developed a common interface system.)
JL doesn't have such a problem with most of oneworld carriers at least even though it is not part of it.