The problem you are describing is horribly common among point leagues. The #1 reason this problem exists is because:
There is no such thing as a "standard" points league.
Theoretically speaking, a points league is better than any categorical league because points allow you to weight events appropriately whereas categories treat them all equally (e.g. - SB = HR). The problem is that most point-league owners get too worried about event weighting and don't think about the pitching-hitting balance (or lack thereof) that you described. If you have to pick between pitching-hitting balance or proper event weighting, always pick pitching-hitting balance. For that reason, practically speaking, categorical leagues are better because they force pitching-hitting balance on a league. They just do so at the expense of event weighting.
If you're willing to put in the time and effort to create a scoring system personalized to your league, shoot me a PM. I'm not kidding, though. It will take a good amount of work on the front end. Point scoring needs to be based on a quite a few factors with the two most important characteristics being the size of your league and the size and makeup of your starting lineups. If you want to go that route, I'll be glad to help.
Want an easy icon?
All you have to do is beat a few guys at picking Sunday's winners.[/url]