I'd rather have the system be completely up to the admins to define the skill trees - what if I want an "electrician" skill for my high-tech server? Or an "undead hunter" skill, that only gets increased by killing skeletons and zombies? Or something related to a completely new mechanic introduced by some mod?
I'd imagine a fully modular system being split into experience triggers and perks, with configuration telling what skill each is associated with and how much XP it provides or requires.
XP triggers would be things like breaking certain blocks, killing mobs, using items, or anything else for that matter - you might even be able to see some of the stuff from MC's own stats system. Perks would let you do more things, like mine better ores, craft items more efficiently, use more things, or deal more damage with each hit.
For example, in your default configs the farming skill might have breaking tall grass as a small-scale XP trigger, crafting a hoe and harvesting crops as a more beneficial trigger, and as a perk let you sneak-click crops to make them grow faster and plant and harvest more different kinds of crop.