Planned functionality of skills created this way:

• Be able to position, have item icons and or custom background or png

• Have parents, use skill point requirements, use level requirement and check for items like skill do

• Be able to awards players items, points (perhaps run a command), attribute modifiers or potion effects

How would u make a mod using JAVA to add onto this

Do you mean how would you use this mod to create a skill tree? Assuming you know how to make a Minecraft Mod you can use this as an example. However, this is not the place for that kind of question.

Why not have a similar setup to Better Questing? Im Sure Funwayguy would be glad to give insight on that end?