Alteration for all the (Oakflesh) spell's child effects. As I said, I've tried all the obvious solutions.

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I have a bound silent bow (i.e. silent casting) that is free of any soul trap. I added this as an alternative to the regular bound bow which automatically casts a soul trap once you accept the right perk (the problem being that sometimes you might want to switch the effect off). It increases Conjuration quite noticeably, hence the question.
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I had another quick look at the introduction to your plug-in, and a question jumped out at me. It seems you've dialed down the casting cost of some spells. It would not make much sense to me if the more expensive spells returned the same increase as the ones that are easy to cast. Is it possible that the low casting cost is drastically slowing the corresponding skill increase?
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What you could do, instead, is return the spell costs to their original level but raise the amount of magicka available correspondingly. Then, for the other side of the balancing act, raise the spell maintenance cost you've introduced to bring the available magicka back down o the target range you have in mind for the ideal spell. You may have to adjust (according to level) either the range of maintenance costs or the factor you use to raise the default magicka level ... or both.
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This sounds like a very interesting mod, and one thing I think might make the magicka side more interesting is setting a limit on how much spellcraft the player can remember (which expands either by level increase, magic school skill increase or a combination of both). This would, naturally, require some kind of non-destructible Tome where the player can "store" disused" spells that are taking up memory (in the form of overall magicka, with the remainder left for casting magicka). It's probably easier said than done, but I think it might fit nicely with what you are doing and something like this may even make the balancing act a little less complicated...
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but that's just my 2c!