I think the short attention span social media has trained everyone to is the problem. Baseball is 9 innings, it is a thinking mans game, pitchers duels and match-ups.
The past 3 years has been nothing but bashing, trashing, WWE style interaction on the political level and I think it's bled over to sports.
Baseball, aside from when Lou went on a rant over a call, is not full of dust ups and name calling. Were there any dugout clearing flairs during the Boston - NY games?
I have no answers for the ratings situation, it does not have the anger appeal NFL and politics does.

Aside from the length of the games, my big issue with Major League Baseball is the lack of a salary cap, and thus, the lack of parity between the big market teams and the small ones. It's not a direct correlation, but the teams with the highest payrolls tend to make the playoffs more often than the ones with smaller payrolls. A lot of the appeal of sports is watching the drama of the underdog trying to upset the favorite. In the case of the MLB though, that's pretty much been taken out of the picture since the playoffs end up usually just being matchups between the same few favorites - Boston, NY, Detroit, LA, SF, etc. - which kills ratings.