<--- also another hobby dev that goes the "equip skills" route, although the skills are tied to equipment bought in shops as opposed to purchased with JP from a menu.
Always felt the martial classes in the original Final Fantasy got a bad deal. Magic shops were interesting, but there wasn't much variation to the fighter, thief, and black belt other than "hit harder".
So, the weapon shops are more like magic shops and the magic shops sell different wands, rods, and staves as opposed to spell books.
Skill organization is kept really simple, since the player is only going to have a maximum of 4 skills per skill type at any time.
The skills at the top of the list is the "simple" version with the lowest resource cost, and the second is the "strong" version with a greater resource cost. The last two tend to be "hidden skills" acquired by having a certain combination of equipment on the actor.
In the DB, each weapon adds a skill type and a couple skills.
There are also a few accessories that add skills to a particular skill type. This creates the "hidden skills" that the player will not see unless they have both the weapon adding the skill type and the accessory adding the hidden skill.
As an example:
A heavy shield would have a "shield" skill type added to the equipped actor and come with a single defense buff skill and a whole party defense buff skill. A ring of fire protection doesn't add the "shield" skill type, but it does add a "flame barrier" skill to that skill type.
So if an actor has just the heavy shield equipped, it has the two basic shield skills. If it also equips the ring of fire protection, it will see a third skill added to the "shield" skill type. If the player doesn't have the shield and just has the ring, they don't see the hidden skill, at all.