I think it's good to point out that part of the increase in HRs is due to the launch angle craze, which is partly due to the increase in shifting. But I don't know that it's that easy for batters to simply "smarten up" to beat the shifts (by going the other way). The pitchers have also changed their strategies to some extent to try to force batters to hit into the shift - they mentioned this in one of the playoff games I was watching the other day. So that would make it harder for the batter to simply go the other way. I don't know that all these hitters are necessarily pull-happy - I think to some extent their swings are just based on where the ball i pitched. I think we've seen a lot of this with JBJ.
But if pitchers are pitching inside somewhat more to get batters to hit into the shift, it also leaves a lesser margin of error - if they miss their spot inside, and leave it a little over the plate, then there's a greater chance that that ball is going to be taken deep, more so because of the hitters' launch angle approach. So I think the long ball may be the most effective way to attack the shift, other than maybe bunting (a lost art, but that's a different story - I hate the sacrifice bunt, but I'd like to see a lot more bunting for base hits).
On a side note, I've also noticed that all these shifts are having an odd negative impact on my enjoyment of the game. It used to be that "going up the middle" was one of the most basic rules or approaches to hitting, and certainly a good way to try to get out of a slump. And watching the game, when you see the batter hit the ball up the middle, you're immediately thinking "that's a base hit." But with all these shifts, balls up the middle are frequently just outs. As a fan, I find this frustrating, as in my mind these "should" be hits.