How tall are you?
If you're tall (5'11" or taller), you might experience fatigue over time due to the riding position of the R3. The fact that the R3 is a cross between a standard and a sport bike means you'll be hunched over most of the ride (especially if you install a rear set which inherently moves the foot pegs toward the rear).
What kind of work do you do?
If you work physical labor, then you might want something more upright or even relaxed; back pain, muscle aches & strains don't jive well with the sport bike riding position, especially if you're a tall rider.
What is your weight fully geared?
If you are heavier than 165lbs fully geared, you'll want to invest in some suspension upgrades (I don't know anything about the 2nd Gen R3 (2019-2021), but the 1st Gen R3 (2015-2018) is severely lacking in suspension. Furthermore, unless you like the fairings of the 2nd Gen, save your money by buying a 1st Gen and upgrade the suspension that meets your weight.
I wrote a bit on cheap
suspension upgrades. However, the bit on the Ninja 650 rear shock may be discomforting.
How far is your commute?
If your commute is greater than 20 miles one way, if you buy an R3, invest in a seat like the
GP-V1 by Saddlemen (verify model fitment). The stock seat is a pain in the ass. Also, the stock windscreen isn't formidable for tall riders (or maybe even any commuters in that case); you may end up choosing to purchase a
double bubble windscreen.
Alternative Choices
Also, I would test ride the
MT-03 if I were you; that bike with a windscreen might be a better choice as a commuter. Look into other upright motorcycles as well. While the MT-03 does sport an upright seating position, it is a "hyper naked" sport bike; which means there are no fairings (which may not be favorable at 60+ mph (highway speeds).
Arguments in Favor of the R3
Reasons I would recommend you buy the R3: If you're a weekend or seasonal rider, are shorter than 5'11", and don't work a physically laborious job (like construction or night stocking).
Conclusion
Unless you fit the description of the Japanese Yamaha R3 rider to the T, you'll be spending a pretty penny on modifications to make it
fit you. If that's what you want, do it! If not, then ask yourself what you truly need and do some more research into a beginner's sport upright. I don't have many good examples as I haven't done much research on it (maybe I will update this post with other options in the future).