Started a CBS Dynasty H2H League last year with the scoring below. Ended up working out nicely! The goal was to have each individual players stats speak for themselves (ie. didn't matter if they were on a good or bad MLB team). Using this scoring system 57 of top 100 were pitchers. This compared to 33 pitchers in the top 100 rankings for 2014. Could see tweaking the numbers a little, but it's pretty close for a first stab at it!
Scoring for Batting Categories Name Settings
1B Singles 0.92 points
2B Doubles 1.50 points
3B Triples 2.06 points
AST Assists 0.01 points
BB Walks (Batters) 0.60 points
CS Caught Stealing -0.44 points
GDP Ground Into Double Plays -0.16 points
HP Hit by Pitch 0.60 points
HR Home Runs 2.80 points
KO Strikeouts (Batter) -0.1 points
OFAST OF Assists 0.10 points
OM Outs Made -0.27 points
PBC Passed Balls by Catcher -0.19 points
SB Stolen Bases 0.19 points
Scoring for Pitching Categories Name Settings
1BA Singles Allowed -0.92 points
2BA Doubles Allowed -1.50 points
3BA Triples Allowed -2.06 points
B Balks -0.19 points
BBI Walks Issued (Pitchers) -0.4 points
ER Earned Runs -1.1 points
HB Hit Batsmen -0.4 points
HRA Home Runs Allowed -2.80 points
INN Innings 2.25 points
IRS Inherited Runners Scored -1 point
K Strikeouts (Pitcher) 0.2 points
PKO Pick Offs 0.44 points
WP Wild Pitches -0.1 points