I have been thinking about the flaws in Third Edition Dungeons and Dragons (and Pathfinder 1E) because I am trying to do better in my own version of the game, Labyrinths and Liontaurs. Here are some of my biggest kvetches with the skills system, and my ideas on how to do it better.
Mechanics in General: 3E Dungeons and Dragons had a worthy goal -- to make it more likely that some classes used some skills, and other classes, others. But the way they did it, with a cross-class rank system that required tracking skills gained by each class per level, with half ranks in there, was crazy complex. Pathfinder simplified the game by removing/consolidating skills and by making all skills easily accessible to anybody -- but at the cost of oversimplification, making some skills "way better" than others, and losing the tendency of some classes to use certain skills. My solution: Impose a non-proficiency penalty to use non-class skills. This is like the -4 non-proficiency penalty for using weapons with which you are not proficient. You can gain skill proficiency by your class, by a trait, or by a feat. ALSO, cap the ranks you can put into a skill at character level (for class skills) and at character level minus two for non-class skills. That's not as harsh as the limit of half your character level used in 3E, but it still means that spending on class skills is required at levels 1 and 2.
Game Balance in General: My preference is for in-game choices to be balanced, that is, if you choose option A, you end up with about the same power level as if you had chosen Option B. Now, the 3E game and its successors have always had some skills that are "better" than others -- you see it in that some skills are just much more widely taken than others. My solution: Break skills that are too good into seperate skills (thus unconsolidating some of those that Pathfinder mashed together), and add utility to others by expanding what you can do with them. My goal is to make all skills more nearly equally useful and valuable.
Let's talk about some specific skills. You can find my versions of skills by clicking from the Labyrinths and Liontaurs Skill List.
Spot, Search, Listen, Perception: Third Edition carried over a legacy from the earliest days of the game: Hide in Shadows, Move Silently, Detect Noise, Open Locks, and Find/Remove Traps. In 3E, that became Hide, Move Silently, Listen, Spot, Search, and Disable Device. Pathfinder simplified most of that down to just Perception, creating the "best" skill in the game. But Perception really IS too good. My solution: Group all senses together into a passive skill (Spot, based on Wis) and an active skill (Search, based on Int). That cuts the value of PF's Perception in half. I'm retaining a couple good consolidations from Pathfinder: Move Silently and Hide into Stealth, and Open Locks and Remove Traps into Disable Device.
Let me elaborate on the difference between my ideal versions of Spot and Search. Spot is automatic, and happens when you are not trying. Search is what you use if you are actively working to sense something. Spot never takes an action. Search always takes an action. You can't intend to spot something -- its use is instinctive and instantaneous. You intend to Search for a trap or a hidden compartment, or a footprint. When an invisible creature is walking towards you, roll Spot to see if you sense its approach. When you have a reason to suspect that an invisible creature is in the area and you are trying to perceive it, use Search. In general, you are more likely to find something when you are searching, compared with finding it by gut instinct, if skill ranks and mods are equal.
Speak Language, Linguistics, and Scrivening: Both Third Edition and Pathfinder adopted the "spend a rank, learn a language" philosophy. I always thought that was unrealistic. Pathfinder also added some stuff to Linguistics, which I think should be broken out. So I am adding a Language skill and a Scrivening skill. The former lets you make checks to understand, speak, and read a language, with a DC20 to sound like a native. The latter I broke away to cover forgeries, cartography, sketching, and codes and ciphers. Hopefully that's enough to make it an attractive package.
Sleight of Hand: I've added utility to this skill to include juggling and to allow you to juggle weapons in combat.
Heal: Players who are new to the game are often disappointed with this skill. They expect that taking this skill will actually make them useful healers. But the specificity and limitation to particular use cases in fact makes this skill hardly useful at all. Pathfinder tried to solve this problem with the Treat Deadly Wounds part of the skill, which they added. I've taken that a couple steps further.
Jump and Tumble: I unconsolidated the Pathfinder Acrobatics skill. It covered too much, and breaking out Jump gave me another strength-based skill. And I got rid of the CMD as DC to avoid AoOs thing. That was lame. Yes, there are some skills that are not opposed. Sense Motive to get a hunch at DC20. Picking a pocket. And yes, tumbling to avoid an AoO. I have no problem with that.
Break: Break was already practically a skill in 3E. All the DCs were already spelled out. All I had to do was formalize it as a skill. A new strength-based skill, for extra gravy.
Use Rope: Classic example of a 3E skill that did too little. I brought it back and added utility with DCs for moving with a rope and a couple handy extras.