My solution was to add Alertness. It was the one area that wasn't well defined by a skill and that I was struggling with in game play. So my simple 3x9 skill chart had to expand to 4x9.
That's right, 9 skills. At least for Fantasy Skill20. Different settings could require different skills around subjects such as magic and technology.
Skills replace numbers such as Base Attack Bonus (use Melee or Ranged skill) as well as defenses. Without numbers derived from levels, there's no need for levels. Advancement is handled through advancing skills and stats. Advancing skills is fairly easy, growing more difficult with higher skill ranks, while advancing attributes are expensive and require a lot of work (xp).
The third part of the character building blocks is the selection of feats. Class abilities from other d20 incarnations are part of feats, as well as some familiar feats. The initial number of feats hinge on stat scores and are gained by improving stats and getting skills to certain break points (11 ranks of a given skill). Feat gain is fairly slow, though the initial helping may look generous. However, given that the player uses feats to emulate class abilities, they can get used up quickly.
The player can decide whether to focus their character and make it more versatile based on feat selection with the obvious trade off. The same holds true for skills. If a player dumps all xp into advancing their melee skill and load up on combat feats they will shine in toe-to-toe fights. The counter to this min-maxing is to have a well-rounded campaign with plenty of skill checks and challenges other than combat.