Another way is, instead of just deciding what spawns based on the player's level, you take into account other factors as well, such as Armor, Damage, Magic ability, etc.
Then you can spawn enemies respective to the player's level and with some positives or negatives based on how the player is built. If a player is level 10 but has 300 Armor because of the crafting system, you spawn a level 10-15 mob that may have additional damage, or can bypass armor via their own perk.
You can also create enemies that have abilities such as Dispel, or have more enemies Disarm, etc.
This design has a lot of problems as well.
For starters, it eliminates the player's freedom to choose more or less difficult gameplay, it neutralizes the differences between different character builds, and it potentially eliminates the benefits of many of the perks. As it is, if I want to RP a 'normal' person, I use less powerful equipment and spells, choose fewer combat perks, etc., and the game becomes more challenging. If I want to RP a more powerful person, I craft better weapons and armor, use the best spells available, and put my perks into combat. In your design, this would no longer be an option.
If you scale the difficulty to every aspect of the character, you will experience very little, if any, variability in difficulty, regardless of your character's build and the equipment you use. Maybe that's how you would prefer to play the game, but if anything, it just seems like a more intense version of Oblivion's scaling mechanic. I, for one, would hate a scaling mechanic like this, so I don't see how it's an improvement on the current system. It would make my current build, which is designed to be as difficult as possible, impossible. It's just a different system that appeals to a different play-style. What's the point of using better weapons and armor and picking combat perks if the result is that your enemies become more powerful? Your perked out warrior will have as much difficulty in combat as your peace-loving merchant. At least with the current system enemies actually do feel tougher if you don't build your character for combat. The whole point of designing a good combat build is to be better at beating enemies than someone who doesn't. If there's no advantage to building your character this way, then there's effectively no differences between different builds. The same argument goes for improving your weapons and armor.
Also, how do you prevent players from exploiting it? I can just walk around in my street clothes with no weapons equipped, wait for the spawns, then equip anything I like. There's no way to reliably scale based on gear. You can say that those kinds of players are just spoiling the game for themselves and it won't affect the majority of players, but that's the same argument you can use against crafting. I don't abuse it, so it's never been unbalanced in my game. Ever.
And scaling against Health/Magicka/Stamina would accomplish nothing, though it might imbalance the game even more. These stats are approximately equivalent in value. If I have a high Stamina, I can carry more/better gear, sprint out of harm's way, and powerattack my way through enemies. (The people who think that Stamina is somehow a worse attribute to invest in are the people who've never invested in it.) Scaling against attributes wouldn't produce an effect that is different than scaling based on the player's level, since every character is going to have the same number of points based on level. Ie. it's a redundant mechanic.
Note that I'm not saying that the game doesn't have design issues (there are plenty) just that I don't think
more scaling is the answer. The real problem is that there isn't enough of the right kind of alternate content. It's not viable to create a non-combat character because there isn't any content to support it. Stealthy characters don't need to have the difficulty scaled down to their level (after all, where's the excitement in sneaking past enemies you can easily defeat in combat?) they need content tailored to their skills and perks that is inaccessible to non-stealth characters, the way that bone-crushing free-for-alls are inaccessible to them.