If you do not need the speed I might go with the box way machine due to the fact it will have a longer machining life, in my neck of the woods Hyundai's are are far more common than Yama Seiki. I know guys who have 15+ years on there machines and can not see the purpose of buying another machine because they have had such luck. Though Im sure there are companies who have had the same luck with Yama Seiki, Haas, Mazak, Mori, ect... with today's technology its hard not to buy a good machine tool. Everyone is using similar components, Fanuc drives, NSK ballscrews the list goes on, yeah some companies have their own conversational control, but the basic construction is very similar. Do what you feel is best for your company, both machine tools are great.

What materials do you plan on cutting? The reason being is both machines you are looking at are great machine tool. The Yama Seiki being a box way, while the Hyundai is has cross linear roller ways( giving you the rigidity of a box machine but the speed of a linear machine. Yama Seiki was the OEM builder for Toyoda VMC for several years. If you spec the Yama Seiki vs a Toyoda they will be equivalent in all spec besides the front window. To me I feel both machines will get the job done it really depends on what materials hardness you will be cutting. I would see if you could get a test cut on both to compare apples to apples. Best of luck.