If something in the game is flawed then it's a bad game design. I'll give an example, Attributes in Oblivion were horrible, they interfered too much with leveling, and if you didn't power level the game got harder. Now from what your saying you would want that type of system in Skyrim because you liked it, even though you know that it's a mess and would cause the same issues that occured in the last game to occur again. That also is the same thing with SpellMaking, it causes a lot of problems because people exploit the system whether it's something harmless as a a second spell or something more dangerous, it's going to happen. Sure people can limit themselves but why should they have too. Fallout 3 had that exact same problem no matter how much I held myself back my character is still going to get broken.
Who decides what constitutes "flawed." The need to carefully choose which attributes to level came from a REAL flaw in the game. Poorly managed Level Scaling of NPCs. It was Level Scaling which also made spell making almost essential for mage characters, because after level 30 or so, NONE of the games purchasable destruction spells, AND VERY FEW of the games target-other Illusion and Alteration spells were OF ANY USE against the mega-powered enemies you began to encounter at every turn.
Undead who NO turn undead spell that you could find or buy without making would effect. Trolls, Ogres and goblins who swallowed the strongest vendor/merchant/trainer offered fireballs and lightning bolts like they were jelly beans and gummi-bears. In Oblivion, a mage without spell making was relegated to being someone's b*tch or someTHING's breakfast.
The beauty of spell making wasn't that it made you an invulnerable god. It COULD do that if you REALLY micromanaged the hell out of it ( in which cas you earned your reward) or used glitch cheats, in which case you didn't give a damn about "balance" anyway. The real value of spell making, however, was that it allowed a pure mage, or predominatly mage character to keep up with the game at higher levels. A master wizard who had the power and skill to cast an extremely potent charm spell, strong enough to briefly mesmerize a Dremora Kynmarcher , or to create a firespell that would actually make a goblin chief think twice about charging after him, or cast an encumbering spell that actually slowed his enemies down, rather than having them laugh at the notion that they ever imagined they couldn't shrug off an extra 35 pounds, could NOT get his hands on any of these things, despite having the power and talent to use them, UNLESS he resorted to spell making. And shouldn't a Master of the magical arts be able to figure out how to tailor make a spell? I mean, really, to hell with, "is it still balanced to be Uber challanging even at level Grade AAA+ MegaGrandMaster status?", whatever happened to plausible ROLEPLAYING? Why should a master wizard, or master anything else, be an incompetent, mediocre peon, for the sole purpose of constantly giving the player a hard time. Isn't that what the difficulty slider is for? Your GrandMaster everything character too mighty for your liking? Start a new, neophyte character, or go back to a save file from when you were level 4.
As to spells automatically gaining power with leveling as a solution. . . what happens when you don't want to use a spell that is literally overpowering (i.e. a spell that literally goes far beyond the boundaries of what it's caster wishes it to do, in a way that is contrary to the caster's intentions).