I, on the other hand, will make another argument and then I will offer some conjecture. My argument is that we are not seeing a rise in home run rates around baseball. What we are seeing are home run rates exploding for middle infielders. Gone are the years of Cesar Izturises and now we welcome our Jonathan Schoops. Below is a table with HR/PA rates and percent change from 2015.
A paired T-Test with Middle Infield included reaches significance at 0.03 while excluding the Middle Infield balloons it to 0.16. Meanwhile, a comparison with the National League renders a greater jump with values of 0.0002 and 0.003, respectively. Group it all together and both wind up as significant with 0.01 and 0.04, respectively.
Below is a graphical representation of how each position league-wide is impacted. DH (not shown) is tucked into Total and Total without Middle Infielders.
So, the great home run explosion is largely the result of the current crop of middle infielders slugging the ball better than last year's batch. Roughly, the leagues are seeing a 40% increase in home run hitting from those positions. That is what is happening. Now, some conjecture on why it is happening.
While the safe path is to simply call this a remarkable coincidence with so many young exciting middle infielders this year, such as Jonathan Schoop, Manny Machado, Trevor Story, Marcus Semein, and Roughned Odor. However, I wonder to what extent defensive shifts come into play here. For instance, a player like Jonathan Schoop benefits greatly from a shift. His main detriment is a lack of range while his greatest defensive advantage is his strong arm. As such, he can play deeper back and utilize a shift to take advantage of his arm and reduce the impact of his limited range. By doing this, you can get his bat in at second base when before you would need to rely on a more defensive player who likely has a worse bat.
Again, it may just be the ebb and flow of talent has decided to backwell into the middle infield. Or maybe it is a concerted effort to let guys with good bats stick in the middle infield until it is evidenced that they really do not belong there at all. To a lesser extent, you also see the increase in other shift position like third base and center field. If you batch position by shift impacted (2B, SS, 3B, and CF) vs. minimally impacted (C, 1B, LF, and RF), you see some stark differences. Home run rates increased for the shift position by 25% (p=0.006) while minimal shift increased by 2% (p=0.19).
As it stands, it seems untrue to blame millennial pitchers. It seems highly unlikely that there is some new wonder PED. It seems curious that a new ball would impact only certain positional hitters. It seems likely that for one reason or another players who are most employed with defensive shifts are those who also have a much stronger bat than those in years past.