Some good suggestions, but I think you missed the point I made about game balance:
If weapon attacks are converted to skills, then ALL attack rolls need to be converted to the same formula. I suppose for ray attacks and attack rolls made as part of casting a spell could just use the caster's effective CASTER LEVEL as the BAB for it (skill rank). That would probably work.
Similarly, if saving throws are the only thing that's not converted, then yes, spell DCs don't need to be converted either nor do special attack DCs (though special attacks that require an attack roll do). But that's an IF THEN clause.
SPELLS KNOWN/PER DAY
I'd prefer to use [caster level + casting stat] to predict a set number of spells known and spells per day than just the casting stat. That sort of encourages specialists (which I really want to see more of in the game). Spells per day could probably be [1/4 highest caster level + casting stat modifier - spell level] = spells per day of each spell level. So a 20th level character with a 25 casting score (+7 stat mod) could hypothetically have 3 9th level spells per day but if they only had 19 (minimum) they'd only have 0 per day. Encourages casters to NOT be minimalists (you know those casters who put everything into CON/DEX and only dump spare change into the casting stat to keep up with the minimum and just cast spells that don't allow saving throws, I HATE those guys).
SKILL FOCUS
How do we handle how this makes Weapon Focus and Spell Focus worthless and Skill Focus a GOLD MINE? What about class abilities that provide skill/attack boosts? Their effectiveness is also manipulated.
SKILL POINTS
How do we handle these extra skills? Do we just give everyone 4-6 more skill points than normal at every level?
So let's try this...
ATHLETICS (acrobatics, climb, escape artist, etc.)
CRAFT (alchemy, devices, metalsmithing, etc.)
KNOWLEDGE (dungeoneering, engineering, history, etc.)
MAGIC (arcana, spellcraft, use magic device, etc.)
SOCIAL (bluff, disguise, diplomacy, etc.)
WILDS (handle animal, heal, survival, etc.)
+
3 new groups
WEAPONS (subskills are particular weapon groups and non-magical special attacks)
Your BAB with any weapon is equal to your ranks with the weapon GROUP. Weapons that overlap (appear in multiple groups) use whichever is best.
Weapon Groups (16): http://www.d20pfsrd.com/classe...C-Weapon-Training-Ex-
Combat Maneuvers: Each type has it's own skill except those that already use a skill (like Feint which uses Bluff or Disarm and Sunder which use Weapon Attacks).
*Only specific weapons are added as class skills based on the class's weapon proficiency.
SPELLS (subskills are particular spell descriptors, subschools or schools baring descriptors)
Your CASTER LEVEL with any spell is equal to your ranks in the spell's school.
Spells (Abjuration)
Spells (Conjuration)
Spells (Divination)
Spells (Enchantment)
Spells (Evocation)
Spells (Illusion)
Spells (Transmutation)
Spells (Universal)
*Spells are added a class skill to any class capable of casting spells (not SU or SP abilities).
OR
No spell skills. Instead, convert existing skills into spell skills therefore making otherwise "mundane" skills more combat-useful. Athletic skills are already combat-useful (escaping things, avoiding AoOs, outrunning things) and weapon skills are obviously combat-useful.
Abjuration: Knowledge appropriate to creature type affected (if affects specific creature type), Craft appropriate to item type affected (if affects specific creature), Knowledge (planes) (dimensional anchor and other abjuration effects that specifically manipulate dimensions/planar travel/teleportation).
Conjuration: Heal (healing), Craft appropriate to item created (creation), Knowledge appropriate to creature being called/summoned (calling/summoning)
Divination: Perception (scrying), Sense Motive (mind reading), Appraise/ Knowledge/Spellcraft appropriate to information desired (all other divination)
Enchantment: Bluff (Confusion), Perform (any)(Charm & Emotion), Diplomacy (Compulsion) Other (GM discretion)
Evocation: See Other.
Illusion: Disguise (glamers), Intimidate (phantasms), Bluff (all other illusions)
Necromancy: Intimidate (fear, curse and pain), Heal or Craft (alchemy) (death, disease, poison) Knowledge (religion) (all other necromancy)
Transmutation: Craft appropriate to item being transmuted (petrification or if targets items), Knowledge appropriate to creature being transmuted into (polymorph or anything that targets creature), Knowledge (planes) (teleportation), Knowledge (history) (time stop or similar effects)
Skill-boosters: Any spell that directly boosts an Int-, Wis- or Cha-based skill (such as Disguise Self, Identify or Glibness) is dependent upon the skill that it boosts. For example, your caster level with Disguise Self is equal to your Disguise rank, your caster level with Identify is equal to your Spellcraft or Appraise rank and your caster level with Glibness is equal to your Bluff rank.
Universal/Other: For all other spells, create a new skill for each descriptor: Acid, Air, Cold, Darkness/Shadow, Earth, Electricity, Fire, Force, Light, Sonic, Water. If the spell has no descriptor and doesn't fall into a category listed here, the GM may use their own discretion to assign it a skill or create a new skill for it. Knowledge (arcana) is recommended for Wish/Limited Wish and Knowledge (religion) is recommended for Miracle.