I have a very elegant solution and wish to share.
This system works no matter which version you run.
I have eliminated the thief class and replaced it with a class called Expert. Expert works exactly like a thief regarding saves, hit points, and all other relevant aspects of the thief class except for the following differences.
Experts can re-roll any one roll they make, once per session per level. This is to support their playstyle niche which is risk-taker.
Experts select 5 skills from the following list. They do this instead of gaining their default skills. I use Skills: the Middle Road* as the system in my game because it doesn't tie skills into level, but X in d6 or % both work. Each level the thief selects a new skill, or raises a skill from skilled to expert to master.
The key to this following list is each of these skills resolves a specific in game 'lock'. It is a literal toolset as the magic users bag of spells, or the fighters bag of murder.
Agility/Athletics: For resolving feats of derring do.
Alchemy: For the creation and identification of alchemical items.
Appraisal: For determining the value of objects in the dungeon.
Arcana: For the identification and use of out of class magic items (wands/scrolls, etc.)
Backstab: For doing additional damage in combat.
Healing: For restoring hp to comrades after a battle.
Listening: For gathering information behind closed doors.
Nature Affinity: For calming and working with animals. This also allows you to use your charisma to have animal companions in addition to henchmen.
Poison Use: Use, identify and treat poison.
Campaign Specific Lore skills: Specifically useful skills that provide additional info in your campaign.
Sleight of Hand: Picking pockets, palming, and other feats of prestidigitation.
Stealth: Hiding, Movement to surprise monsters, and taking a round to set up a backstab in combat.
Stonelore: Identification of slopes, new construction, sliding walls, pit traps depth underground and stonework.
Tinkering/Devices: Disarming traps on chests and doors. and working with machinery.
Note that searching and parley are not on the list by design. The X in 6 chances to locate secret doors once players have given up looking and reaction rolls are not systems that are improved by allowing people to become 'skilled' in them. It is highly likely those will become 'skill taxes'.
The difference between these skills and the usual assortment, is that each of these provides a specific in game mechanical use. There aren't skills for flavor or background (those should be non-mechanical in nature). The system is expandable for subsystems you might use in your campaign
*All non-supernatural tasks have a target number of two to seven. Those unskilled may attempt a task by rolling a d6. Those skilled at a task roll a d8. Those that are experts at a task roll a d10. Those that are masters roll a d12. Target numbers may be modified situationally.