Visit the machines, get your quotes. Establish what you need, make sure you understand the running costs of each, the availability of service personnel & parts - see who wins. The answer won't be the same for everyone. Also see which software you like the best, if you are likely to want any of the optional software features make sure they demo them too.
The Fuji is modular by design, you build up feeder capacity & speed by putting multiple modules together you can then tune your line by fitting the heads most appropriate to the task or if you have the resources even swapping out modules. The capability of the line is therefore not fixed but leaves you with endless way to spend money on options... Most of the Fuji heads are rotary turrets so you should get a more consistent place speeds across different jobs compared to the Yamaha. Some of the Fuji head/nozzle options offer possibilities you might not be able to do with the YSM itself.
The Yamaha is in someways simpler, it only has two head options and even the faster one is pretty flexible. However once the machine is configured with a certain head, that's really how it stays.
Both are respected manufacturers, personally if I had a good idea exactly what work the line was going to do for the next few years, or it is a dedicated line for specific product range I would go Yamaha. If I was expecting it to be in very high demand with much less predictable board types going through it, I might choose the more tweakable Fuji line.
However I think I could be swayed either way whatever scenario was in play if the price or service for one was significantly more compelling than the other.