Hi Jeff Bloomer,
Adopting to CJA definitely has some challenges and limitations.
1) Stitching multiple Event based datasets (lets say Adobe Analytics which as ECID, CusotmerID and Campaign Activity data which as CustomerID, ActivityID). This is especially a challenge in Field based stitching of CJA (needs special Stitched dataset), graph based stitching forces us to enable certain datasets into profiling on RT-CDP even if the requirement is only CJA specific for analysis purpose only.
2) Adobe Analytics eVar, Prop names not auto populated in CJA. Any change in name or addition of eVar and props needs to be updated on CJA side too. - Not sure if there is already a work around for it, will be happy to learn about it.