It is worth noting that although 3e has menu-style elements, few of those elements are actually significant compared to the abilities the basic class has.
Weapon Focus is great, but by 20th level, the specialised fighter has a "massive" +2 bonus to hit and +4 to damage from feats, whilst from the class the hit bonus is +20, and the damage from magic weapons (not related to the class system) dwarfs that of the feats.
Many of the other feats are so specialised in usage that the greater bonuses just come up infrequently. (e.g. Whirlwind attack requires precise placement of opponents.)
For a menu-based system, you have to decide how much "spellcasting" is worth. When you come to major components of the system, this become very, very difficult.
As Umbran and Psion note, synergies are not taken into account. Or, if they, most menu systems get around them by assuming a point cost for the synergy.
We, in fact, have this in 3e. Has anyone played an Ogre Sorcerer? No? Why not? Oh, because the Level Adjustment is way too high? Yes, indeed. It assumes the Ogre Barbarian or Ogre Fighter combination, not the Ogre Sorcerer combination.
Take the Evasion ability. It can be valued at a certain amount because of the good Reflex progression the rogue has. Is that value still valid for a character with a poor Reflex save?
The complexity of the interaction of the major abilities is something that is very, very hard to balance from a point-based viewpoint.
However, with an archetypal class you can examine the abilities in relation to the other abilities the class has and thus decide whether the class is balanced.
Of course, multiclassing (a menu-based feature) distorts this somewhat, which is why the 3e designers made so many mistakes with 3e - all those toploaded classes (ranger, barbarian, etc) which characters would only take a level in... with 3.5e, the implications of the hybrid system that 3e uses were more clear and the adjustments could be made.
One of the chief reasons I prefer the archetypal class system is that the classes are more efficient than those created by a menu-driven system, and, knowing the abilities that the class has gained, you can be more inventive in the higher level abilities the class gained without worrying about them being inappropriately gained by other characters.
Cheers!