Hi there!
The flaw is an easy find: when you have perks like smithing that which are increasing your level but adding nothing to your combat strength we have a problem.
No, we don't.
At one time in the game i had 30 block, 60 one hand, 60 light armor, 75 smithing, 70 enchanting, 60 Lockpicking, 70 speech and 50 restoration(and some other non combat skills on 30-40). As you see about 325 skill points are coming from non-combat-skills. And only 150 from combat skills. This means: 2/3 of my level is coming from nothing then skills that dont help me to fight.
That means you spend 2/3 of your time improving non-combat skills. The bandits and monsters you face spend a much larger proportion of their time gaining combat experience.
1. If i only train my combat skills, my level is much lower but my combat efficiency is much higher. That means: more damage against lower level mobs in cause of the level scaling. This makes the game for pure combat chars too easy.
But your gear is worse, with the exception of lockpicking, since lockpicks are more important than the skill.
2. The opposite is it makes the game harder if you train too much things who add nothing to combat. Without any good reason. Why should the combat difficulty be increased if you train speed, smithing and lockpicking too much? This makes no sense at all.
Yes it does, you are training to be a blacksmith, the enemies you fight are training to be combatants. Combatants beat blacksmiths in fights, unless the blacksmiths superior equipment makes up for the skill difference.
3. Think about mixed chars like thieves. Sneaking is hard already. Until about 50-60 you don't have a real chance to sneak up to someone without being noticed(at reasonable speed and with light armor) So you train about three additional skills like pickpocketing, lockpicking and sneaking. And the only reward is that you have a hard time with your enemies since they are strong, you have only light armor and sneaking is very weak.
Which is why you rely on lockpicking/pickpocketing to buy strong gear, possibly including invisibility scrolls so you can end fights quickly using sneak attacks.
4. You are not stronger AT all if you bring TWO Handed Weapons, ONE Handed Weapons, Archery, Destruction and so on all to the same level. You can't use your bow while casting spells. And you dont use a two handed weapon while you use a one handed weapons. So why do you need to face stronger enemies if you train them all equally?
Okay, you could argue for overlap between 2H and 1H weapons. But switching between ranged spells and ranged bows, becoming excellent at neither, while your enemies focus on just being good archers or just good mages means your enemies should be stronger than you. Training 1H and archery makes you stronger in a different way. You can do some damage from afar, and don't need to run when enemies get close.
Final Question is: why would anyone scale your enemies based on your pure level?
Because they want an open-world RPG rather than a linear RPG and want to add strategy to character development.
I think there is a mistake in your thinking process!

Oblivion had something similar. Your level were increased with your skill-ups, too. The difference is that you had the attributes back then. You trained for example Repair, Lockpicking and pickpocketing and got the possibility to increase for example strength, agility and speed on level up. So: even when you've trained only non combat skills you got stronger in combat anyway because strength and other attributes increased your combat skills, too.
The flaw in Oblivion was that you were punished for using primary skills, because you would level up without enough attribute points to assign.
There is a chance to get your level-scaling to work, anyway. What would you think about a secondary(internal) combat-rating. Based On this combat rating you level your creatures and items. Not based on the overall level.
The combat rating is calculated based on 4 of your combat skills: 1. skill is the highest armor skill(Block, Light Armor, Heavy Armor). 2.+3. skill are the two highest weapon skills(magic schools of destruction and conjuration is counted as a "weapon", too) 4. Skill is the highest crafting skill. (Potions, improved weapons and a perfectly enchanted armor makes you stronger in combat, too). So you have up to 400 skill-points. You can now use this Rating to determine the enemy strength and loot quality. :hubbahubba:
I think it would remove the strategy from character development.You would go from having good and bad decisions, to having good decisions and power-maximizing decisions.