Right now, it seems likely that spell making is out, so improving that is not likely to happen. But alchemy and enchanting are in, so Bethesda can still work on improving those.
I do agree that in past games, custom spells, potions and enchantments never really felt like your own unique creations, unfortunately, I don't really see an easy way to fix that, because the problem, I think, mostly comes from the fact that your options are basically boiled down to a number of generic effects. You can mix and match different effects, and create ones with different strength, but you can't truly do anything you won't see in the premade options, it just might be stronger, or combine more effects into one potion or enchantment, however, I can't really see any sort of system fixing that without being very complex and very hard to program. At least if you got to actually design your own custom weapons and armor, you might be able to get a fairly large variety of fairly unique options available by choosing from a list of shapes for different parts and changing their color, size, texture and such, I'm not saying we'll be able to do that, but it I think it would be possible to do, but what makes a potion feel unique really comes from what it does, while different potions having different appearances is helpful for differentiating them, a potion still won't feel unique even if it has a unique model if it doesn't do anything any common potion won't do.
No, but they WILL have a form of crafting for each of the three archetypes: Stealth, Magic, and Combat.
I expect potion-making, enchanting, and forging, but I haven't put any thought into it.
I'm pretty sure it's been confirmed that alchemy, enchantment and smithing are the crafting options available for stealth, magic and combat respectively. And The only thing I can see them doing is allowing you to make potions, create enchanted items, and forge weapons and armor, as well as repair them, I'd presume.