I have two suggestion for the next set, one for the game in general and one exclusive to the online version. The second might be deemed a little petty, but the "problem" has occurred in my last three tour events.
1. Bring pitcher's injury history from the season into the game. In the traditional methodology, we can expect Joba Chamerbin to have a great card, be e starter/reliever, and perhaps carry a price tag of $7.5mil. I'd like to add some realism into the equation and price him with his true value to the Yankees ($4.5mil?) but have a real risk that he'll sit out half the season.
2. A pet peeve of mine in the online game is the additional power afforded the teams in the West. In perhaps 3 out of every 4 leagues in which I play there's one team that holds up the autodraft for a long time after the 11th team is in. For tournament play, I would be in favor of having the option when setting up the league of excluding the 12th team from waivers for 24 hours if it is entered more than 24 hours after the 11th team.