How about the option during your draft set up to mark what position you would like to have as the main backfill for a player if you miss them in the draft.
For example...
I want Bonds at 13.22m but always planned to play him at DH with his 4 in LF. Instead of giving me the next best LF it takes the next best hitter.
or...
I want Musial at 11.06m to play first, so when I miss him I get the next highest 1b instead of CF where he is listed 1st on his card.
And to add to add to that would be maybe the option of adding what side of the plate you prefer for the fill in - Next best Righty vs next best overall which may be a Lefty. Can't count the number of times I tried to build a team one way or the other and ended up with a reverse team coming out of the draft.
Those are good ideas. The counter to them is that the current situation adds to the skill and challenge of preparing a draft roster. They often don't like to make things easier for us.