My understanding is that they came to realise that I3s offer the same sharp throttle response as their much vaunted cross-plane crankshaft. It also allows for a cheaper, lighter, more compact motor with a power curve that more people appreciate over the peaky output of an I4 (though I still prefer an I4). They will also help to differentiate Yamaha from the pack, giving them a more Euro-flavour (something Suzaki/Homaha are desperate to achieve so they can ask more $ for their bikes, like BMW, Triumph, KTM, Ducati et al.)
The strange/sad thing is, they went and designed the FZ-09 to a cut-rate price point again, with annoying details like the digital tach, cheap suspension, basic electronics, and generic looking headlight. So the value is good, but it's not remarkable in any way so it doesn't elevate the brand.