Synchronization and timing issues are two different things, though, and synchronization is implicit if you get the timing right, unlike emulating hardware on software. The timing aspect of it is just a matter of properly emulating the behavior of the chip; not easy, but significantly easier to get right than synchronization in software.

But that said, FPGAs are by no means a silver bullet. There are a billion problems with them, mainly due to the terrible development tools, at least the ones that someone not doing this stuff professionally can afford.