In order of importance (although not necessarily ease of implementation -- I realize some of these ideas have been suggested and dismissed in the past as way more trouble than they're worth to code. But this is a wish list thread...):
1. Show pitcher's Hold Runners rating in the pitching widget.
2. Separate day/night locations for player and ball locations in the ballpark editor.
3. More flexible inter-league scheduling (i.e., don't always play the same division every year).
4. Better UI for ballpark editor (especially next/previous park buttons).
5. More playoff options (double-elimination, league winners play each other, etc.)
6. Single game and team record books.
7. High school feeder leagues that feed some players into the professional draft, others into a draft for college feeder leagues.
8. Customizable home field for World Series (top seed, alternate years, or all star game winner).
9. Allow human managers who won LCS in previous season to manage all star game.
10. When filling out rosters directly (i.e., not through the draft), give the option of preferentially generating players from local region.
11. Double headers and rainouts.
12. Ballpark quirks. Obviously, this has to be fairly limited, but there are still a couple things that you could do based on what the game knows about the parks:
- Penalties for turf teams playing on grass and vice versa.
- Balls getting lost in the sun (outdoor day games only) or against the dome (more like for visiting team).
- Long indoor homers landing on catwalks.
- Balls bouncing off speakers (indoors) or, very, very rarely, the dreaded Dead Seagull Play (outdoors).