Missing spells that shouldn't be -
Jump - Come on. You know why we want it. For the fun factor. Jumping is already in the game, why not give us the ability to make it a little more uh, interesting? Yes I DO want to be running toward a fort and literally LEAP over the wall and land right in front of my surprised foes. I honestly have no idea if it can be implemented or not, but I sure would like to see it, if it is possible.
Featherfall - So many high places. So many times I want to just run and take a dive off the side of said high place and NOT die when I land. Fun is fun

Night Vision - No spell to help us see in the dark? Magic should be able to replicate the Khajit power.
Silence - Make it expert/master level, only for the dedicated spell caster and lord, make it AOE

Weakness to ____ - Yeah so destruction spells do not scale well, fine. Let us inflict weaknesses to elemental damages so those destruction spells can pack a bigger punch. How about attaching weakness to an element to the rune trap line of spells? Lay a fire rune trap, enemy triggers it and has increased damage to fire for 10 seconds or so. Heck, how about improving the 'rune' perk to inflict the weakness instead of laying a rune 5x farther away, which is not a good perk!
Some changes to existing spells -
Cloak spells - Confer a resistance to damage of their type, eg flame cloak gives 50% resistance to fire damage on top of its damage effect.
Magelight - Blinds enemies when cast on them, satiating the desire to have a 'blind' spell in the game. Perhaps a 25% chance to miss from normal magelight and maybe 35% when dual casted?
Oakflesh, Stoneflesh, Ironflesh, Ebonyflesh - Redo these spells. Why invest in 3 perks to triple the power of an armor spell when you can just hold out a little longer and get the 80% reduction to physical damage spell? Would like to see Oak give 10% physical resistance, Stone give 20%, Iron give 30%, Ebony give 45%, and Dragonhide give 60% reduction to physical damage, and have the perk associated with these armor spells add 5, 10 and 15% more reduction to physical damage, making the best spell cap out at 75% with perks.
Raise dead spell line - Stinks. Why look for a corpse to raise, or have to kill one enemy first when you can just throw down an atronach and if/when it dies, throw down another? Raise dead line should have permanent until killed duration, and when dual cast raised they should be more powerful. The two perks should be changed, perhaps something like giving your undead poisonous attacks, increased attack speed, a larger health boost than 100, or something along those lines.
One last thought, Would love to see some unique spells that are high end rewards (perhaps DLC here folks) that would be on par with getting an artifact reward. Think of it as an artifact spell. Perhaps put small cooldowns on them like the way shouts recharge, so as to balance their awesome power.
One unrelated thought, concerning shouts. How about a perk tree for shouts?

If I posted things already suggested, my apologies.