the answer is simple :
HIGHEST VALUE COUNTS.
now let me explain what this means in detail:
the reason the crafting gets out of hand is you can have FOUR entchants of the same sort on your gear at the same time. and ALL four count adding up to insane numbers in dmg or zero manacosts etc etc etc.
simple change it so that effects you get from GEAR ONLY (effects from perks and other permanent abilitys should not be traded like this otherwise you get racial balance issues + problems with the standing stones aswell) are handed so that only the HIGHEST value one takes effect e.g.
if you have 45 35 and 30 fortify alchemy .
only the 45 fortify alchemy thing will take effect at all the other can be there but wont give you any benefit at all.
if there are four of the same effect value e.g. 45 45 45 only ONE of them counts.
this would fix ALL current balance issues with the crafting entchanting and alchemy and smthing.
tough one problem remains at the end : smithing
some say smithing is op on its own because you can get the best items early on and that very easy. well thats true. but how to balance this? well sadly that thing is not the fault of smithing itself think about it after reading the text below.
smithing itself actually would be FINE IF skyrim had enough UNIQUE items that had 3 or even more entchants on them and that have similar strength to deadric ones or even better like back in morrowind days (the fact you cant upgrade deadric artifcats for example even with the deadric smithing perk seems like a simply oversight to me and should just be changed since it makes sense).
this would reduce the power of smithing while it still remains useful so that someone who does not skill smithing has worse dmg than someone with smithing which makes sense in the end because smithing should grand an advantage when it comes to weapon dmg and armor rating.
this can only be "fixed" by adding alot of new unique items with good entchants on them either via dlc or patches/addons.
let me hear your toughts.