ffs. you get to the point in skyrim where you think you're invincible (even though i've done very little in the plotline - god DAMN i did not expect that much side-questing), and then you wander into a den of mages and three shocks later you're dead. even though i'm at 94 destruction and MY shocks knock of maybe 5-10% of their health. i suspect there are undisclosed game mechanics ****ing with me.
Resist magic and spell absorption are your friend =)
I actually just had to up the difficulty for my Ryne character because I'm at level 51 and very little was posing much of a challenge any longer... though the enchanted dragonscale armour and dragonbone weapons had a little to do with that - and my resist magicka is now so high, coupled with the spell absorption from the atronach stone and Alteration of 100, that only physical attacks are really of any concern. Once you reach 100 Smithing and 100 Enchanting, even without abusing alchemy much, you are very difficult to kill and have an unlimited source of income (take iron dagger, enchant with banish and paralyze on petty soul gem purchased from court mages, makes 1000s of gold in profit).
Though, like you, I've done very little of the main quest - I'm only on Diplomatic Immunity. There is SO much to do in this game.
As for the game mechanics, spells do not level up with your skills - skill only reduces cost, not power of spells. Destruction in particular requires perks and the highest level spells to be of any use. I pretty much abandoned destruction magic by level 15 as a result. Also, the dual wielding perk is mandatory for destruction in order to get the stunlock effect. See here:
http://www.uesp.net/wiki/Skyrim:Destruction