So I was making a new companion and I thought it'd be easy... Just basic 2 hand stats, combined with a decent magicka pool, and high destruction as well as high skill in 2 handed. I even made the combat style spellsword and heck even made the chance of magical attacks or whatever to be 10 with melee as a 4, but no matter what this NPC will NOT bother using the fireball spell. The NPC would even use a heal spell, but still refused to use fireball even after I deleted the heal spell.

Is there some issue where NPCs that use two handed weapons, don't want to use destruction spells or something?

Assuming you used the existing Fireball spell, this has a minimum skill level of 50. NPC's with a lower skill level wouldn't use this spell.

Was your companion's destruction level equal or higher than this?

Strangely enough it was at exactly 49, I knew about destruction requirements, but for some reason the NPC was a lower level than I intended causing destruction to be too low... Anyways thanks for bringing that up.