Weapon enhancement bonuses may still need to exist, but apply only to damage and crit dice. This makes using a higher level weapon better, but not enormously so, especially for special-effect weapons like Skyrender or Fey Slaughter that you carry to negate monster abilities rather than do damage. This bonus could be made inherent and/or mundane by way of masterwork weapons if you prefer.

Another option might be to buff the hell out of Weapon/Implement Focus and just bake it all into that. Putting an extra tax on PCs that use multiple weapons and implements is the downside to that one.

If I'm reading it right, the only boost to attack rolls and defences would be ability score increases. So you'd get a +4 bonus over your whole adventuring career. This would also need to be reproduced by masterwork or similar heavy armours so they don't fall behind on AC. I do like retaining some channel for upgrading items; rewards are still important and sometimes they need to be tangible.