Another issue that I keep running into is that despite everything, without some artificial cap on Weapon skills, attack bonuses are going to quickly outstrip AC. Since I don't really want to make changes to how AC is done or introduce some fudge factor that treats weapon skills differently, here are a couple of more mods to the BAB as Skills rule:
The Parry - instead of being a feat, any character can divert any amount of his weapon skill towards AC - as long as he is wielding that weapon and is proficient with it. The only caveat is weapon size. Any modifier diverted this way is modified by size - one size difference gives a -2, so it takes at least 3 points diverted to make any impact on AC, and 2 size difference bestows a -4. More than 2 sizes away and you can't parry with that weapon. So a greatsword has as much difficulty parrying a dagger as a dagger a greatsword.
The Multiple Attacks - weapon skill can be split up to a number of times equal to the PCs dex modifier. So with a dex modifier of +3, and a +7 Dagger Weapon Skill, you could do an attack at +3, an attack at +2 and another attack at +2.
The Parry - instead of being a feat, any character can divert any amount of his weapon skill towards AC - as long as he is wielding that weapon and is proficient with it. The only caveat is weapon size. Any modifier diverted this way is modified by size - one size difference gives a -2, so it takes at least 3 points diverted to make any impact on AC, and 2 size difference bestows a -4. More than 2 sizes away and you can't parry with that weapon. So a greatsword has as much difficulty parrying a dagger as a dagger a greatsword.
The Multiple Attacks - weapon skill can be split up to a number of times equal to the PCs dex modifier. So with a dex modifier of +3, and a +7 Dagger Weapon Skill, you could do an attack at +3, an attack at +2 and another attack at +2.