That's the nature of the beast my friend. The other 20 or so weeks of play should even everything out.
You could always abandon H2H play and switch to roto..
I totally agree that roto is a better measure of the overall ability of a team. However, when you're playing with friends, it's more exciting to have direct matches with them twice a year. Thus, it's hard to convince everyone to switch.
My league happens to have two teams that are head-and-shoulders above the rest of the teams. The margin between me and the other team is razor-thin, and it annoys me to realize that this week will probably settle who takes the top seed. Considering most teams pitch 50+ innings in a week, I don't get why they don't just set the requirement at 18 innings, or 1/2 the normal requirement, or something.