I think the times a runner won't score from first on a hit-n-run double are pretty slim.

If anything, I think the game advances players too much most of the time. Some of it may be based on the disconnect between the description and the actual happenings, but in particular a few too many guys go from 1st to 3rd or 2nd to home on singles to LF, a few too many players advance from 2nd to 3rd on groundball outs to the leftside, that sort fo thing. And players almost always score from second with two outs on any outfield hit.

To me this combined with low clutch pitching ratings (where pitchers will do worse with men on) is what can create the big innings that are maybe a little too big, in particular with 2-outs. How often do you see a man on second score on a single, with the batter going to second on the throw, then he scores on a single by the next batter, who advances to second as well...