We've mentioned skill points before. You get a few of them every level. The really good skills are class-exclusive, like a Priest's Heal, or a Bowman's Rapid Fire. A few other skills can be learned by a certain classes. Most of the fighter-type classes can learn Power Attack, and most mages can learn Shield.
Some skills, like Climb and Jump can be learned by everyone. They cost more for some classes than others. Thieves can learn these skills for one point per rank, as can dancers. Crusaders and Fire Mages pay two or three points. If you have two classes, you pay the lower amount. Some characters, when they take another class, get a couple skill points back. If you were a Fire Mage with had four ranks in Jump, and decided to become a Fire Mage/Thief, you'd get 8 skill points back.
Everyone gets the same number of skill points - things get too complicated if we do it any other way. When we want certain classes to progress more slowly, we just have their skills cost more.
We've mentioned movement skills. Is it fair to have areas that certain characters can't go to? I think so. It's balanced by those characters being less powerful. There wouldn't be whole dungeons or cities that are inaccessible, but there might be a few treasure chests or some healing items that you need these skills to get to. Again, it's in everybody's interest to have a balanced party. Or spend the skill points to make up for it.
If you don't have climb, you can still go up walls, but it takes a bit longer and you might fall back down. Jump, however, you can't fake. A character who has passed an obstacle can help others cross, though.
Each rank in a skill costs the same amount. Otherwise, eventually you have to save up for five or ten levels to go up one rank, and it's bad form to have the characters remain stagnant for long periods of time. Going from rank 2 to 3 in Increase Spell Range costs the same as going from rank 5 to 6.
Some skills have caps. If the most difficult cliff in the game requires Climb 5 to go up, then we shouldn't let people put 6 points into it. Power Attack is unlimited, for instance, as is Heal.
Skill points are adjustable. You get four each level. You can adjust those points until you gain a level. Then they're locked there. Let's say you're level 8. You get your four points and use them to buy Jump 2. You find that it doesn't get you anywhere special. You can put those four points back and use them to buy something else, like Defense Dance or Axe use. And if you have those four points invested when you hit level 9, they're stuck there. Perhaps you can readjust one 'stuck' skill point each level.
If you hold on to your points, like Brisbane did, only the most recent four are adjustable - otherwise, the smart thing to do is take all your points out right before you level up, every time.