From what I noticed, the HB's like MJD AND Adrian Peterson do better over the corse of the game while teams with not so great half backs (Packers, etc) get hammered a lot more running the ball. I just had a game with sdrian where he ran for 130 yards off 23 carries however I also have had him run for 50 yards on 20some carries as well. I like how it makes you game plan a lot more. As for QB percentages try bumping the Pass Reaction slider or turn the catching slider down.
Over the course, (Im on week 11-12) I am having a great year however my Completion Percentage is a 45-50%. The highest is Brees with like 60% while the lowest is my other friend in the league who has like 40%.