You can use attributes on items to apply buffs to skill levels.
This works by hijacking the attribute setting its name to the desired skill, example as follows:
/give @p leather_chestplate{AttributeModifiers:[{AttributeName:"skillz:item_bonus",Name:"skillz:melee",Amount:2,Operation:0,UUID:[I;1170423212,2071743757,-1220810514,1287223732],Slot:"chest"}]} 1
That is an chestplate that gives an additional 2 skill points to the melee skill when worn.
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