I don't doubt they've got bugs relating to large trees, but that is not the sole source of the problems. My tree has only just over 1,400 names, and about 100 pictures, and it failed to sync again. I had added names and sources and synced successfully earlier in the day. But then I changed a name (adding a previously unknown last name) and added two pictures and sync failed.
I just unlinked and nuked my online tree again. Will upload again tomorrow, if I get 'round to it.
BTW, I regularly 'compact' my FTMM2 tree to keep its indexes (or do you say indices?) in good shape, and that does nothing to prevent sync failure.