There was no reason in the whole wide world for spellmaking to be removed, the balance argument falls apart when you take a look at how easy it is to tip the scales over through smithing and enchanting.
The difference is, using enchanting and smithing "normally" isn't overpowering (or shouldn't be, if balanced properly). Spellmaking, on the other hand, welcomed overpowering effects with open arms. Spellmaking was essentially a crutch, it was Bethesda saying "we can't make anything better as you level up, so do it yourself". There was no "normal" way to handle spellmaking beyond making powerful spells, and this is in conjunction with mages already being insanely overpowered at high levels. The entire design behind spellmaking screamed for abuse, while enchanting and smithing have a more meaningful purpose to it than being a god-mode-enabler.
To me personally, removing spellmaking was the Big Bethesda Blunder? for Skyrim. Since Oblivion, they have made at least one major screw-up or gameplay change that received an overwhelming negative reception and they have admitted to. Oblivion was the level-scaling, Fallout 3 was no continuation after the game ended, and for Skyrim, I have a feeling it will be the removal of spellmaking. People are spewing venom over it being gone.
I would say the quest system is a much bigger blunder. Magic can be salvaged by tweaking the buffs and how it scales, and bringing in more useful spells (which can be done via DLC), while the quest system is poorly designed from the ground up. Enter a city, get a ton of quests dumped on you without warning, and being told "if you don't want to do it, just ignore your ever-filling quest log". The miscellaneous quests are a step down from Oblivion's in terms of writing, the pacing of the main guilds is abysmal, the quest log provides almost no information besides pointing right to your target, and the dialog leaves much to be desired. Fixing this would require going back over almost all the quests, rewriting them so you can get a proper journal history, modifying them to pace better, adding the option of declining them as appropriate, and possibly recording the extra lines to deal with this (though if you're desperate, I bet there's enough prerecorded dialog that you could fit something in). The much-touted Radiant Quests were also handled much better in Daggerfall, over 15 years ago (although the core idea is good, so it can be improved still).
Ultimately, I don't see the quest system being salvageable by DLC (I mean, who would want to pay for a DLC that adds next to nothing and only fixes the existing quest system?). The magic system can be better handled as DLC as it would mostly deal with some tweaks, and add plenty of new content (extra spells, more quests for mage characters, etc).
Maybe the quest system could be salvaged by a decent expansion (Morrowind's expansions vastly improved the in-game journal, even for vanilla content), but from what I can tell, Bethesda doesn't seem that keen on doing big, sweeping expansions that also changes vanilla content anymore.
Compared to Daggerfall, yes. It's quite literally the difference between a game the size of Great Britain vs a game the size of a fair town.