Both manufacturers have a history of leaving their owners with nasty bills for quality/design issues outside the warranty period. The big difference is that whilst you can go through many of the Yamaha models from F115 through to F350 and find examples of this (at least one leading to threats of class action in the US courts), the Suzuki cases that I am aware of have been limited to just a couple of models and year groups.
I am not enough of a gambler to buy another F series Yamaha. Having had 3 of them to look after, that is what my experience tells me buying a 4th would be. So far we are batting 66% in spending big money to sort out generic design/manufacturing issues of F series Yamahas. I don't know that Suzuki have a much better attitude, but they seem to have better design/quality control based on what has been happening in the real world.
The cost of owning an engine doesn't stop at writing the purchase cheque, and the cost of fixing some of the issues that Yamaha have had has been $1000's rather than $100's. Are the current series engines better than the last series? The dealers will tell you yes, but only time will tell the real story, as it did for the previous models.