For weapons, I agree BAB should be linked to a skill not your character level. I would also suggest you check out WoodElf's alternative weapon proficiency system - it just rocks! In addition, why not make Combat Manuever into a skill? Ranks in Combat Manuever allow a PC to offset penalties usually associated with a particular move, e.g. disarm, feint (replacing Bluff), mounted shot, etc.
Another thing to consider is whether certain feats will give access to exclusive skills (like in ArsMagica). Possibilities include Weather Sense, Dowsing, Scry, or even Literacy if literate characters are rare outside the nobility. For example, by taking the Scry feat, your character can now gain ranks in the Scry skill as if it were a class skill.
Another idea discussed on these boards is to divide a skill into three parts (like Feng Shui). Take Ride for example. Ride (Dex) determines your ability on horseback. Ride (Cha) determines your contacts in the horse world, including furriers, stablehands, breeders, etc. Ride (Int) details your knowledge of various breeds, evaluating a healthy horse, recognizing famous horses/riders, knowledge of horseback contests, etc. So the Cha-modified ability represents contacts, and the Int-modified ability represents knowledge pertaining to the skill. This requires a bit of work, and may be difficult to apply to skills like Gather Information. (I am working up a document to explain how all PHB skills would look in this skills system)
My last idea is specialization. Whenever a player takes a skill, have them declare a specialization appropriate to the skill. Whenever attempting to use the skill in their specialization, they gain +1 on the skill check. This provides more customized characters, at the cost of extra book-keeping.
Here are some examples for the Ride skill: Riding unsaddled mounts, griffons, sharp turns, jumping, spurring to greater speed (racing), mounted combat, tricks, distance travel, mounting/dismounting, falling off horse, etc.