Initial thoughts on the current magic system
After the initial read, few things come to mind.
I'll tell you this in two parts. I want you to read the first part, then to forget about it, because the solution is more likely in the second part.
PART FIRST:
'Alter' and 'Complex' are competing. They just do the same thing in a mechanically different way.
'Destroy' doesn't contribute much. It's a simple solution in a complex system. Made 'Range' and 'Wide' it easily becomes too powerful, and it's mostly pointless to make it 'Complex' or 'Sentient' - if we're destroying something, it doesn't matter much how we do it.
'Fire', 'Air' and 'Water' can be lumped under 'Simple Uniform Matter'(or simply 'Matter'). It widens the application of this kind of magic, making it more fun, without having three spheres that feel similar. I believe you already had 'Matter' as a replacement for 'Conjuration' at one point, but what made you change your mind?
PART SECOND:
'Flesh', 'Nether', 'Fate', 'Desire' and 'Space' have potential to be radically different, and change all of the above, as the current system could interact differently with these spheres.
Since 'Fire', 'Air' and 'Water' can be viewed as a single sphere, all that I wrote about them can be viewed not so much as issues of the whole system, but quirks of that specific sphere.
Think about what you want to accomplish with remaining five spheres, and that should define the whole system better.
ADDENDUM (or, 'I wasn't sure where to stick this' section):
'Plant' is too slow to be considered by most players, and only as much fun as Fenestra's fauna. Why wait (al least) weeks to grow something, if you can buy, forage, or steal it? We are adventurers, damn it, not farmers! You could have it as 'that weird tree-magic elves use' for lore reasons, but players will likely discard it as too impractical. BUT! if you tell me I can have a Plant Wizard who grows his own thorn armour that damages enemies, and his armpit mushrooms cause people to hallucinate, and the spores in his saliva remove fatigue, I would think it really cool, but you would have to make an extensive and detailed list of all effects that can be gained from plants, fungi and lichen in Fenestra. Essentially, the whole sphere depends on how fun are the ways in which plants can be used.