Need feedback/idea for skill learning system Options

[Icenick99]

I feel that the heart of all games is the battle/skill system, so I decided to start building a solid base then work in story, maps, characters, etc...

So originally what I wanted to do was create a fantasy world where there are 10 elements, 5 major (fire,water,earth,lightning,wind) and 5 addition combinations (i.e: water+wind = Ice).
The way you would learn skills would be like FFX sphere grid, each character would have some starting point Fire/Wind/Lighting/etc... The whole idea is that healers or healing spells appear only in certain elements such as lighting, defense and tank abilities would lie in earth.

The problem, building a sphere grid is not a simple task, let alone implementing it into RPG Maker. Also there is a lack of uniqueness when everyone can do everything.

To counter this I wanted to include a secondary learning system or unique skill that each character will have (example FF3/6).

Finally I liked the concept the ideas and the spells, however binding it to my story was the hard part. The problem is that the story Im set on and the abilities don't make sense together.

I want to make a game somewhat simpler to X-men, in the sense that your main party will be "mutants" with a unique power set. Taking this approach I feel limits options, if you want healing abilities you need to take the lightning "mutant". You may say well whats the big deal, many rpgs have done this before white mages only learn healing. Also a power set like telekinesis does not reflect well in RPG turn based games, and I dont want the mutants to only be limited to controlling 1 type of element.

First off when I was creating my elements I had a vision, a sense of mastery over an element, such that lightning can shock people, restore life or even create a flash to blind enemies... What im getting at is the lightning grid offers customization so that your hero doesn't have to be a healer if you don't want, lightning in nature does more then heal it can strike you down.
Secondly the learning system would be very linear, even if I allow multiple options and paths to learn different skills. To counter this a job system might work, but again the story takes place in the semi-modern world, with humans, it kinda doesnt make sense to have swordsman, warrior, ninja, etc... jobs. But thats my opinion.

Sorry for the long wall of text. If you stuck it out this far thanks, and in conclusion, I want to bind my story with my element skill system, Im not sure how, some good systems would be similar to espers or materia, but they eliminate my sphere grid idea.
The ideal situation would be to have my heroes have 1 Unique mutant ability, the ability to learn elements and include a job of some sort (job more for the weapon and passive stats, i.e: Theif, Warrior, etc..)

I feel like its too much and doesnt make sense. Any ideas or feedback?