I'm still researching this but the problem is that OOTP is generating too many 3-0 counts vs RL MLB. My sample size is still too small to be definitive but it appears that OOTP is generating just over 3 X 3-0 counts per game. This season in MLB the average is 1.58. I just tracked the last two days on BR and got 47 in 30 games played which is 1.57.
So far it seems that IRL MLB players swing at about 7.5% of 3-0 counts and in my MLB fictional league they swing at 9.2% of 3-0 counts. That alone is not a huge difference but given that the 3-0 rate in OOTP is almost double it's easy to see why one would perceive they swing too often.
I'll check some other RL seasons to see if the rate of 3-0 counts and the swing rate change significantly. If anyone is interested in helping with data try reading about 10 OOTP game logs and tracking how many 3-0 counts you get.

Edit
Swinging on a 3-0 count does happen IRL even in critical situations. See Jayson Werth below. So far this year there have been 240 AB at 3-0, most (all?) of them swings. The results
H 86
HR 22
GDP 6
SH 1
SF 7
ROE 3