I agree - no head-to-head when playing for $$$ in baseball. It works great in football where teams only play once a week and performance for a given game is more predictable. In my opinion, it shd not be in baseball at all - $$$ or no $$$....Baseball players performance on a game by game, week by week, basis are too unpredictable cause they have to play every day....so you can have a great fantasy team, but because half of them are in a temp slump or have nagging injuries, you team does poorly in a given week.....very unrealistic.
For scoring, I'd use standard 5X5 categories - roto scoring.
For $$$ distribution, 55% 1st, 30% 2nd 15% 3rd is average.