The explosion of skills in the Companions and RMSS turned off a lot of my players, and I wasn't a fan. So I came up with a compromise:
1 - Primary skills. Original RM2 skill, plus "Pick pockets" and maybe one more. If a player tries something that would use these skills, but has no ranks, they have a -25.
2 - Approved Secondary skills. This is a short-list of about 15 skills I felt made sense in my campaign, but not at the level they should be "primary." I will ask for their bonus in these, if applicable. If a player tries something that would use these skills, but has no ranks, they have a 0.
3 - Other Secondary. If a player really wants one of these skills, they can develop it. I will never ask for it, though, I'll likely choose a stat bonus and go with that alone. If a player has developed the skill, though, they can volunteer that and get the bonus. Someone with no ranks has a default 0 rank bonus.