This is an issue I've been thinking about way too much. I don't normally like to broach subjects, because I like a wider variety of opinions available to expand upon my understanding before formulating my own. Still, as I play Skyrim more and more, the crafting issues are something that irritate me sufficiently that I feel the need to put something out and get it off my mind. This is likely going to be a rant few, if any, would like to read in its entirety right away, I suggest reading the TL;DR and if something piques your curiosity, positively or negatively, read the entire section of said issue to engage in a discussion proper. Now that that's out of the way, it's time to get down to business.

Smithing:

In my opinion, this is the root, and product of all the crafting issues in Skyrim. I am by no means suggesting that Smithing be removed from Elder Scrolls. It's actually my love of the craft that drives my harsh criticism. I think I've read enough of these forums, while unusually negative for a first-party forum, to know that Smithing is seen by the community as grossly overpowered. But I don't see the problem as that simple, smithing's problem is that there's really no "middle ground" for the craft. You're either totally invested in it, or ignore it entirely. What's more, is it's a craft that doesn't exist on it's own, there's virtually no reason to craft gear without it's sister craft, enchanting, as armor and weapons, both enchanted and unenchanted, exist in nearly every container within the province.

So you have a craft where the simple act of utilizing it breaks the character. Even without investing in perks, the armor and weapon upgrades can become grossly overpowered given the chance. I Play on Master, and have never even tried anything lower, and I still find it hilariously easy to break a character just by using the ability naturally. Exacerbating the issue, is the necessity of Smithing as a form of horizontal progression, with special exception given to mages (Which have their own issues, particularly destruction) smithing is literally an essential skill. I'm not here to debate the fact that you can play the game without using smithing, you can play Skyrim virtually any way and still have success, but the game is designed in such a way that it seems to assume you're using the skill, and by virtue of it's exponential style gains, you can quickly ruin the challenge and thrill of combat.

So you're left in a situation where the game utilizes smithing as a critical means of progression, but a means of progression that used naturally, kills the sense of conflict that permeates Skyrim. Fortunately, I don't see the issue being all that difficult to resolve. The most direct solution would be to increase the thresholds for upgrades. (Fine -> Superior -> Exquisite -> Flawless -> Etc.) but a static upgrade runs the risk of upsetting the relatively tight difficulty curve early in game. A better solution would be to increase the threshold above Flawless, (Epic -> Legendary 1-whatever). I'm not a fan of hard caps. Soft capping (Excluding exploits) leaves room to expand the game for later content, while having better control over the difficulty curve.

That solves only one problem, the overpowered nature of Smithing. What I think is a bigger problem, is how essential smithing as a skill, feels to any character who utilizes weapons or armor. Solving this is much more complicated technically, though it sounds easy. The solution is enabling Smithing Services throughout Skyrim, to upgrade your weapons and Armor, though certainly not to the extent self-smithing can. I envision a situation where town Smiths can work on your non-enchanted equipment for fairly high cost (Say, 1,000 gold per item), but instantly bring the item to "Flawless" status, regardless of character level or material type. Magic items cost significantly more (Say, 2,500 Gold per item), so for an enchanter, it's still better to make your own enchanted items after you spend less to have it modified, and for physical but non-crafting characters, all that gold finally gets used. It also lets low-level characters use gold to stay ahead of the difficulty curve solo, on higher difficulties, but because their skills are likely so low, it won't disrupt the balance.

Another issue with Smithing also draws on Enchanting, which I'll discuss in greater detail within the enchanting section. Suffice to say, Smithing as a craft is virtually pointless without the Enchanting skill as well. Armor and weapons of all kinds, save Daedric, are much too common to necessitate naked smithing as a means of creating new items.



Enchanting:

I have significantly less experience with Enchanting than Smithing, as I'm sure will show here. I can only hope I know enough that my ignorance doesn't outweigh the critical substance of my opinion.

The issues of Enchanting are, in many respects, similar to Smithing. Were it to exist in a vaccum, it wouldn't be so bad. The easiest issue to identify is of course, the game-breaking enchanting combinations, such as the Fortify Destruction (Any magicka school really) cost reduction removing all magicka cost from the spells, regardless of Skills or Perks. Overpowered physical characters utilizing tons of Fortify One-handed, Two-handed and Archery apparel, and of course, the crafting sets I'm sure many people employ to get the most out of their Alchemy and Smithing.

Enchanting itself is a lot less complicated than Smithing, so the problems and their solutions are a lot less complicated as well. Obviously the biggest issue here is the total negation of Magicka cost for spells. It's not so much that it's overpowered, that it breaks the feel of the game in such an extraordinary way, especially with Destruction. Unlike physical attacks, Destruction magic damage does not scale with skill, gear or Perks (not counting new spells, but whatever), so the 100% reduction set removes the only real "Gameplay" of destruction, that is, managing your DPS with your DPM (Damage per Magicka), creating a type of play that means having your eyes glaze over as you repeatedly stunlock a Dragon until it dies nearly a half-hour later. Remembering how homogonized Oblivion's characters felt because of the Hard Caps in place, I am loathe to suggest something like capping the maximum magicka reduction for spells, but that is a potential solution, though certainly such a cap would be very high, possibly up to 90%. Here's where my ignorance of Enchanting may get the better of me, but it might also be possible to enforce a "Soft Cap" By removing the Fortify Magic Skill from the Neck Slot. I've not yet come across an item in Skyrim that reduces magicka cost on the neck, that was generated by the leveled lists. In fact, the only item I can recall may be the Saarthal amulet, which would, if nothing else, be made to be a very unique piece in this circumstance.

The physical attack overpoweredness is much less an issue, especially if you were to assume that Smithing were to be fixed. The only real reason +160% (or even greater with potions) One handed, Two-handed and Archery is so powerful, is because it builds upon an already overpowered Smithing system. My only suggestion here would be to perhaps remove Fortify One-handed from the feet, though Leaving Fortify Two-handed and Archery (Head) with a potential 160% increase. This "Solution" Is more to solve a different, non-crafting related issue, that Archery and Two-handed, though they occupy both hand slots, are not really stronger than One-handed, so they sacrifice Flexibility for an overkill advantage that doesn't even make a tangible difference.

Crafting Apparel is in much the same situation as the Fortify Physical attacks enchantments. They're only broken themselves because they build upon an already broken system. The only option here is to remove one of the enchanting slots from Alchemy and Smithing. (Body for Smithing, ring for Alchemy, while leaving unique items like the Ring of Pure Mixtures within the game). If the root issue was solved though, it's doubtful that these measures would even matter.

Finally, we get to my biggest issue with Enchanting, and it's much like Smithing. It's the fact that it seems too essential to grow your character with the skill and perks, especially endgame. What's more, is that Smithing itself doesn't even have a reason to exist as a craft, without the use of Enchant. There's just too much armor and weapons already available, most of which is usually enchanted, to employ smithing without enchanting. Unlike smithing though, the only tangible solution is to allow, much like previous Elder Scrolls games, professional enchanting services. Obviously, it would be folly to allow professional enchanters to match the player's max potential (Without exploits), as that would render Enchanting Redundant. I'd suggest that the Court Wizards of Skyrim allow (For a hefty sum, based on the Soulgem used, just to give a number, let's say 10x soulgem's base filled cost) a patron to enchant their weapons and armor up to the "Eminent" Level (With a Grand Soul Gem). The list of Available enchantments would still draw upon the same list the player has, as that's an aspect of the new enchanting I'm quite fond of. If You need to, you could argue some mumbo-jumbo about needing to understand what you want the wizard to do, before you can have him create your enchantment. Just as a personal "Preference" thing, I would really like to see Extra-Effect enchanted items (Again, never as powerful as a master enchanter's self-made items) appear in leveled lists, at around the same rarity as we see Daedric items starting at level 46, though "Extra Effect" Enchanted items should be available from the start of the game, albiet at "Leveled" power, much like we see in standard enchanted items. (Not up to Peerless strength though) That's just a personal desire because I love treasure hunting though, not really a solution to any perceived problem.



Alchemy:

If I was ignorant with Enchanting, I'm practically a virgin when it comes to Alchemy. I utilize the skill a lot, mostly for poisons, but I've never invested perks into the skill, ever, so all my opinions unfortunately come from second-hand experience.

My goal isn't to talk about the Fortify Restoration exploit. While I'd love to see it fixed, that's a relatively obscure exploit that one has to go out of their way to abuse. My interest is in things that break the game just by their natural existence, but this is hard with Alchemy, as unlike the other crafts, Alchemy is actually very labor-intensive. Few shops have ingredients in any notable quanitity, and the progression structure is less Linear than Smithing or Enchanting. Where with Enchanting-Smithing, your better gear is a permanent upgrade, and you never have to worry about finding more Moonstone or Ebony once you have your gear, Alchemy's consumable nature, and plethora of effects means you always need to get some out in the field and collect, so believe me when I say that a paralytic poison that lasts for 20 seconds and also does 120 damage over 10 seconds is a justified item in the context of the game. The only part of Alchemy that really concerns me is the abundance of Monarch Butterflies and Blue Mountain Flowers, allowing a great alchemist to mass-produce dozens upon dozens of high-powered Healing potions. Given how many healing potions exist as loot in the game though, that seems relatively petty.

If there are other issues with Alchemy, I'm entirely unaware of them, and look forward to anyone who does see an issue, or differing opinions on what I may not perceive as an issue.



TL;DR:

If you skipped down to this, you were right to do So, the monolith of text I've produced even shocks my own senses.

As a summary though, for Smithing, I strongly believe the anchors for each level of improvement needs to be expanded, and perhaps even introduce smithing services across Skyrim, that don't quite match mid-level player's abilities. Enchanting breaks magic in the worst way, by making it boring without making it seem powerful, Enchanting also seems to be married to the smithing skill, as there's no reason to craft armor or weapons without enchanting to back it up, and the physical enchanting options only seem broken because they compound an existing issue. Unlike Smithing, I deem enchanting services for Skyrim a "Necessity".The Obvious exploit of Fortify Restoration aside, I know very little about Alchemy, save that you can make hundreds of hyper-powered Healing potions with the abundance of easily obtained restore health options. More than any other Craft, Alchemy seems fine, really.