Yes, when you have fully Perked 100 in all three skills and then add enchantments and potions on top of that, there is a big problem, but when you don't take those Perks it is the Potions and Enchantments that make up for it. I should be able to make a decent (but not the best) Healing Potion with a combination of +Alchemy gear and potions without investing Perks into Alchemy and Enchantment.
Anyone with the requisite Skill can upgrade armour and weapons of a given type, the higher your skill the better your upgrade, but someone that can already make Daedric Armour twice as good as anyone else, thanks to a Perk, shouldn't be abdle to make it five times better thanks to using enchantments and potions on top of a maxed out skill constellation. At the same time, however, someone that doesn't have the Perks to make Daedric Armour (which, incidentally, is the only Smithing tier that can be made without investing a single Perk into Smithing thanks to a certain facility) should still be able to improve it with the help of potions and enchantments.
My suggestion is that, instead of removing the enchantments and Potions, or arbitrarily capping them across the board, their effectiveness be capped based on skill level and/or Perks. Someone with 25 and no Perks in Enchantment will get a significant boost from all their +Enchantment gear and Potions, but someone with 100 and maxed Perks will get only a small boost. I think that +25%, from all sources, at skill level 100 is ideal, though +50% might also be okay.
I am not saying that players who do not take Perks should have access to the best crafted gear and consumables, they shouldn't. I am pointing out that the gear and potions that are available are there for players that have not already reached 100 and filled out all the Perks in their crafting constellations (but also that they should still have some effectiveness at 100, just a lot less than what they did at lower levels).
I probably should have had some coffee before writing this, but I hope I made my point.