Take it with a few shakes of salt...
There are two or three problems with the 3e/3.5e skills system. First of all, no one (not even the rogues) have enough skill points to be good at all the things that make up their "job". Secondly, a/n (N)PC can be wrotten at everything their class entails, while being poor, Cross-Class, in something their class doesn't! Worse, they can be totally lacking in skills required for their class (such as a Wizzer with no Spellcraft, who can't learn a new spell from a scroll or spellbook found in the dungeon).
There are two ways to fix this: The Class way, and the Class-less.
The class way breaks all skills down into four categories: Primary, Secondary, Tertiary, and Unrelated. Primary skills are what a class does every day, and MUST be good at. Secondary skills are what they do often, and would be skilled in. Tertiary skills are what a class would have to do, at some point, but not often. They would have some basic knowledge, but not much. Unrelated skills are something a class could safely ignore all their life, with no ill side effects...
Once skills are divided up, for each class, ranks would be added every X levels of that class. Primary skills would be added to every level (like a Fighter's BAB). Secondary skills would be added to every Y levels (1rst, 3rd, etc., perhaps?), and Tertiary at (say) 1rst, 5th, 10th, etc. Unrelated skills would receive no benefits from that class.
The skill points/level would still be received, and could be used to improve class skills, or gain cross-class ones. Which "Group" a skill fell into would depend upon the Class in question.
The Class-less system gets rid of classes all together. It consists of a table which details how many XP an ability is worth (the 2e DMG had such a table, but it would need expanding to cover all skills, HD, and feats). At each level, the PC chooses their abilities and total the XP needed to advance to the next level. This allows for tough mages who wear armor and wield martial weapons (but advance slowly), and skillful, lightly-armored fighters specializing in a single weapon who blaze through levels... It also isn't D&D, as we've known it. Not that that's necessarily a bad thing! D&D aint what AD&D used to be!
EITHER system is flexible and adaptable - something 3.xe isn't.
There are two or three problems with the 3e/3.5e skills system. First of all, no one (not even the rogues) have enough skill points to be good at all the things that make up their "job". Secondly, a/n (N)PC can be wrotten at everything their class entails, while being poor, Cross-Class, in something their class doesn't! Worse, they can be totally lacking in skills required for their class (such as a Wizzer with no Spellcraft, who can't learn a new spell from a scroll or spellbook found in the dungeon).
There are two ways to fix this: The Class way, and the Class-less.
The class way breaks all skills down into four categories: Primary, Secondary, Tertiary, and Unrelated. Primary skills are what a class does every day, and MUST be good at. Secondary skills are what they do often, and would be skilled in. Tertiary skills are what a class would have to do, at some point, but not often. They would have some basic knowledge, but not much. Unrelated skills are something a class could safely ignore all their life, with no ill side effects...
Once skills are divided up, for each class, ranks would be added every X levels of that class. Primary skills would be added to every level (like a Fighter's BAB). Secondary skills would be added to every Y levels (1rst, 3rd, etc., perhaps?), and Tertiary at (say) 1rst, 5th, 10th, etc. Unrelated skills would receive no benefits from that class.
The skill points/level would still be received, and could be used to improve class skills, or gain cross-class ones. Which "Group" a skill fell into would depend upon the Class in question.
The Class-less system gets rid of classes all together. It consists of a table which details how many XP an ability is worth (the 2e DMG had such a table, but it would need expanding to cover all skills, HD, and feats). At each level, the PC chooses their abilities and total the XP needed to advance to the next level. This allows for tough mages who wear armor and wield martial weapons (but advance slowly), and skillful, lightly-armored fighters specializing in a single weapon who blaze through levels... It also isn't D&D, as we've known it. Not that that's necessarily a bad thing! D&D aint what AD&D used to be!

EITHER system is flexible and adaptable - something 3.xe isn't.