I'm just brainstorming here...
List 25 players like you do now, plus
For your first 10 draft positions, you get to do the following:
1. list a specific alternate (optional)
2. check a box to go to your next draft position if you don't get your first pick or--if you have listed one--your alternate pick
If the check box is not checked, you would get "best" alternate as it is done now if you don't get your main or alternate pick. You could choose to check this skip option (or not) individually for each of your first 10 draft positions.
Any skipped picks would be done normally ("best" alternate) but the pick would be moved to the end of your draft list.
If this, or something else, is made available, it should be made as an advanced drafting option. The one advantage the present system has is simplicity.