Here's my attempt:
Chameleon takes a second to readjust to your new background. Chameleons can't instantly change colour they need some time so it only makes sense that you only become invisible if you stop jumping around and if the enemies see where you stop then they still attack you.
Weakness can't be cast in the same spell as the damage type it's weakening the enemy against. If you want to cast 100% weakness to fire and magic you have to go through multiple casts giving them a chance to dodge before you nuke them.
Paralysis should be replaced completely by petrify, it does the same thing except it greatly increases their defence and looks much cooler.
Resist damage shouldn't stack with itself, if you have a helmet of 50% resist and a shirt of 50% resist the engine flips 2 coins if both come up tails you get smacked.
Reflect doesn't block the damage it just reflects it back at the opponent hurting them unless it reflects a spell in which case instead of dropping dead it actually reflects the blast and they have to jump out of the way.
Absorb doesn't block damage it just gives you mana from a spell.
Lightning, fire and frost shield are the only ways to get 100% immunity to an attack while resist magic gets capped at 50%, this will mean they actually get used.
Invisibility can't be cast if you're already in a fight or preferrably since Skyrim is full of snow the enemies can follow your tracks, though this will require much more dev time.
Restore health, fatigue and majicka can't be used in a constant effect.
I think that would greatly improve the thought needed when fighting with spells and prevent players from enchanting a load of gear to make themselves invulnerable.