Who likes spending a feat on a weapon that (with a few exceptions), is not much better than a martial one, especially when you just want it for looks (I’m looking at you katana). Once possible solution is to treat weapon proficiencies as skills.
Essentially you are using skill points to buy the weapon proficiency feat. Each rank reduces the non-proficiency penalty for the weapon by one. A character cannot not devote more ranks this way than they have levels and never more than four ranks for a weapon. A character cannot use this rule to buy other feats.
Weapons which can be used as martial weapons when wielded two handed still count as such. Using the weapon one handed uses the modified non-proficiency penalty.
Weapons which provide a benefit for being proficient with them only provide this benefit once you are fully proficient with them.