Here are some things I'd like to see to make managing teams easier or just to add more enjoyment to the game:
1. Have a place to see all the ML boxscores for a given cycle, not just my own. If I'm coming down the stretch and watching the out-of-town scoreboard, or just seeing what other teams are doing, it'd be nice to have a page with links to all the pbp pages in one place.
2. Have an option to receive a note in my inbox when anyone on my watch list gets a rating change. I like to keep track of my prospects pretty closely, and it'd be nice to know right away when another cycle has completed.
3. When I'm looking at teams' depth charts, player name searches, or trade proposal rosters, add the number of years as a pro as a column on the main display. This would help me quickly determine who the actual prospects are, and who are 5th and 6th year pros with little to no developing left to do.
4. Allow me to add more than one type of icon to a player's name when I add a note to their page. I use that yellow paper icon to distinguish real prospects from minor league filler, and it would be nice to be able to refine that further, or make other easily visible distinctions (such as DITRs, international signings, or players received in recent trades).
5. Put a note in my inbox when my waiver claims aren't successful. Sometimes I get forgetful and wonder whatever happened to that claim I put in. Bonus points if the note lists the end result of the waiver claim (i.e. who did get the claim).