The trend in the industry has been a shift towards Upside Down Forks, however looking at the single R3 teaser is seems like the R3 will be using conventional fork setup, which is odd considering Yamaha's position on USD's...
If you compare the lone teaser to say the new R125 you will notice that the R3 has noticeable bulge down near the axle, which looks quite like a conventional fork set up. Notice the skinny lower section of the R125 with its USD setup...Inverted forks are positioned on the motorcycle opposite or upside down when compared to conventional forks. The leverage forces that cause fork flex are greatest at the triple clamp area and weakest at the front axle. On inverted forks, the large outer tube of the fork is clamped in the bike’s triple clamps and the sliding inner tube holds the axle and front wheel. By locating the large diameter tubes in the triple clamp, the inverted or upside down fork have their largest and strongest parts combating the highest stress. This arrangement gives the forks high rigidity, which improves their response by reducing the side loading of the internal bushings (sliding surfaces). This kind of response is particularly important in high performance applications. Most inverted forks use cartridge-type damping systems.
Also, since the damping mechanisms are now held by the triple clamps, unsprung weight is minimized. Reducing unsprung weight is one of the biggest contributors to quality suspension performance, particularly for featherweight motorcycles like the YZ series or R1 and R6.