I think you could go a long, long way toward simplifying the game and making it more flexible by reducing classes to lists of skills and feats -- with plenty of flavor text for plenty of character concepts.
A Ranger's list of feats (in the same style as the fighter's) might include: Alertness, Endurance, Improved Critical, Point Blank Shot (Far Shot, Precise Shot, Rapid Shot, Shot on the Run), Quickdraw, Run, Skill Focus (Class Skill), Track, Weapon Focus; Nature Sense, Animal Companion, Woodland Stride, Trackless Step; Sneak Attack, Evasion, Uncanny Dodge.
If all classes get one feat per level (period), this isn't too complicated.
But there's a second step that makes the whole thing much, much easier. Instead of providing countless prestige classes with countless new rules, the books could provide sub-classes with skills already chosen and with feats laid out by level:
Ranger of the North
Primary Skills: Listen (Wis), Spot (Wis), Survival (Wis).
Secondary Skills: Climb (Str), Heal (Wis), Hide (Dex), Jump (Str), Knowledge (geography) (Int), Knowledge (nature) (Int), Move Silently (Dex), Ride (Dex), Search (Int), Swim (Str).
Feats:
1 Track
2 Alertness
3 Endurance
4 Woodland Stride
5 Trackless Step
6 Nature Sense
[...]
An Nth-level Ranger of the North would have Primary Skills with N ranks, Secondary Skills with N/2 ranks, and Feats 1 through N. (I'm assuming we also toss the notion of first-level being special, with extra skill ranks, quasi-feats, etc. A starting character would be 4th-level.)