New engine manufacturing technologies, tight tolerances, materials used in bearings, rings and cylinder walls, coupled with the cleanliness of factories today, fine surface finishes applied to the cylinder wall and reciprocating bearing surfaces, and factory initial fire up processes - mean that there is virtually nothing in the oil and filter after 600 miles, except oil. Just stick to the factory specs. 600 miles for the first oil/filter change.
The engine/trans is designed to operate on Yamalube 10W40 and 10W50, that meets both API SG and JASO MA specification (MA2 is aplos applicable as it exceeds the MA rating). This indicates the intended specific oil is Yamalube FS4, which is fully synthetic. Interestingly, the SG specification is obsolete, so we can assume that SN or SP will be adequate as the modern standard - however, API specifications do not cover motorcycle engine oil use directly. The JASO MA standard, which covers engines where the engine and transmission share the same oil, is actually more applicable in the case of the R3. This includes their MA2 rating, and now the latest T900 and T903 specification. At this time, the following oils meet both standards:
Yamalube GP Racing Spec 4T
Yamalube HP High Performance 4T (available in a change kit with filter)
Valvoline 4-Stroke Synthetic Motor Oil
Mobile 1 Racing 4T
Amsoil Synthetic Metric Motorcycle Oil
Motul 300V 4TMotul 3000 Plus 4T
Motul 5000 and 5100 4T
Castrol POWER1 4T
Castrol Actevo Synthetic Motorcycle Oil
Castrol Actevo X-Tra T
Silkolene Pro 4
Silkolene Comp 4
Silkolene Super 4 (semi-synthetic)
While there are many who feel that any motor oil will work, and will attest that they have never had a single issue running whatever brand they find at the auto parts store, there is no harm putting in a little extra effort to utilize a proper motorcycle lubricant that covers the needs of the gear box and clutch, rated JASO MA, MA2, T900 or T903. I have personally found that Yamalube gets the job done, and have been running it in pretty much every motorcycle I have owned for years, including Kawasakis and Aprillias, etc..