One particular issue I've encountered is that syncthing 2.x does not work well for systems w/o an SSD due to the storage backend switching to sqlite which doesn't perform as well as leveldb on HDDs, the scans of the 6TB folder was taking an excessively long time to complete compared to 1.x using leveldb. I haven't encountered any issues with mixing the use of 1.x and 2.x in my setup. The only other issues I've encountered are usually related to filename incompatibilites between filesystems.
syncthing is not perfect, and can get into weird states if you add and remove devices from it for example, but for my case it is I think the best option.