Destruction is messed up because as you advance, the "low level" spells are no longer used. And some of them (flame, spark, frost) are really cool spells that just have no application outside of killing skeevers at later levels.
It's a completely messed up skill, and it deserves more thought than has been put into it. (Note: I am not saying it needs to be more powerful, it needs to be fixed.)
Does magicka even affect spell power or damage anymore? In Oblivion and MW one of the side effects of a huge magicka pool was your spells became godly. In Skyrim there is no point in putting points in magicka past a certain level because with enchantments you get free casting and no damage boost.
Also, in Skyrim, as you level up you leave the old weak spells behind and use the new ones. Seems backwards, as a mage's spells should ALL be useful as he/she learns the arts.
I still use flame, frost and spark against select mobs, and most often use Firebolt against just about everything.
Another odd this is that some spells, like the runes, are bad the moment you buy them, but because of their insane cost, you can't even use them until you get the perk for them, even though by the time you're high enough skilled to get the perk, the enemies are scaled too high and the rune does crap damage for the mana cost compared to spells like Lightning Bolt.
Runes aren't really meant to be mana efficient. You cast and recharge, then go into battle. They're useful as a last line of defense, or when combined with Throw Voice. Or--and I haven't done this yet--weakness to [element] potion (fired from a bow) and led into [element rune].