I am at the hobby level with genealogy but have used FTM since the early days. The tree sync seems to be the area with the most potential for problems but it is getting better all the time and they have addressed many of the problems. I like it because I can invite contribitors that I know to work on my online trees and I can sync and backup. For my peace of mind, I mostly work in FTM on my desktop and and sync down occassionl work on the online trees plus the things contributors may have added. Then I keep good backups from my desktop program. This keeps the volume of work on my desktop which I trust pretty much.
Things I do to keep a healthy environment:
Compacting and closing/restarting FTM before a sync. Maybe overkill but until I am confident treesync is rock solid seems to increase my percentages of trouble free syncs.
Shutting down and restarting computer at least 1 per week.
Cleaning up the hard drive 1-2 times per month.
I have a tree with about 20k persons and really don't have many issues. There could always be some issues that I haven't uncovered but I don't think so. The heavy duty users will certainly have their opinions.