It's been awhile since I've looked at it so I'm a little rusty. Here are some thoughts off the top of my head that would be great:
Editing All-Star Teams without duplicating players
re-alignment of teams, editing their logos, names, etc
adding uniform and uniform slots, and smart detection for the database limitation for number of uniforms that can be added, which uniform slots place things like player numbers in different spots, etc
I like Jim's suggestion about portrait detection, but think along the same lines with cyberfaces - would be good to quickly look up what slots aren't being used, and identifying the special slots (such as the long hair slog used for Randy Johnson/Johnny Damon)
Smart detection for the database limitation for players
adding and editing player audios (which by the way, with AI, we can now easily create pretty much any player audio)
If you want to get really nifty: the option to use a database of alternate portraits and cyberfaces to make it quick and easy to install
Ability to load and edit multiple rosters at one time, so you can literally drag and drop players from one roster to the next, etc
Crash detection is key. I think you know very well from MVPedit that it's easy to edit something that will crash the game. Without the knowledge of editing the dat files along with MVPedit, it can be cumbersome to create a roster. We all know there are things you can edit in the dat files that you can't do in MVPedit, such as the pitch speed limitations. Especially with a lot of current players throwing above 100mph these days.