There is no level chart for all spells. Some have been revealed, but the rest are just speculation.
http://dishonored.wikia.com/wiki/Supernatural_Abilities
We at least know the confirmed spells and that every spell will have two levels. As of rune cost, Time Bend is the most expensive but we don't know if the second level of the spell (Time Freeze) will require more runes or less to upgrade.
OK, let me try and run you through the spells I have knowledge of:
Blink - Level 2 of the spell increases distance, first level free
Dark Vision - Level 1 just shows guards and their vision cones. Level 2 shows objects and sound emitted.
Devouring Swarm - Don't know anything about a level upgrade on that one. It still has one but I believe they haven't mentioned it yet and how exactly it improves the spell. Maybe the rats can't attack you? We'll see.
Possession - Level 1 controls Rats, Fish and Wolfhounds. Level 2 improves the duration of animal possession as well as giving the opportunity to possess humans (Tallboys included).
Time Bend - Level 1
slows down time. This is important to note because if you go in front of a guard while the spell is active, he will get suspicious and security devises like Walls of Light will still burn you to a crisp. Level 2
stops time altogether and is probably the best stealth spell in the game.
Windblast - Don't know about that one either. Don't think it's improved version has been mentioned.
Enhancements (passive abilities): Adrenaline (speculated) - This enhancement isn't 100% confirmed but what we do know is when you are in battle you build up adrenaline. When you reach your max the screen will get a little orange-y and fuzzy, like a bad signal on a TV program and you can instantly kill a guard (if you hit him) when your adrenaline is maxed, going through his defenses. Those effects are minimal so I doubt they will bother anybody (check the latest videos to make sure). Since it is just speculated to be an enhancement I don't have more info on it. It might turn out to be an innate ability but I doubt it.
Agility - Level 1 improves your jumps. Level 2 adds a double jump mechanic + the improved jumping.
Celerity - improves running speed at the cost of vision. You will probably be extremely fast if you use this one and the screen will probably get blurry. No word on the second level.
Feather - Level 1 removes falling damage. Level 2 removes the stun when you fall to the ground. Although it's true you can evade falling damage with Blink and Possession, this spell is a passive not making you worry about timing your Blink every time you make a huge leap and it is faster overall. It's Level 2 is really good.
Healing (not sure on the name) - OK, so this one is tricky. I don't know much about it besides the fact it will give you an automatic heal. Whether that is the level 1 or 2 effect I don't know since there is also something that can give you more health overall. It might be a bone charm or it might be the first level of this enhancement and the second is auto heal. I don't know.
Shadow Kill - Level 1 turns bodies to ash on silent kills. Level 2 turns them to ash no matter if they were silent or have already spotted you. The new trailers showed off that as well. Corvo was fighting guards head on, killed one of them and he turned to ash very quickly. Also with the gas mask guys where they were chasing him and he shot one of them. My favorite ability in the whole game. Some might not like the ash effects but they do fit the art style. The spells is a questionable buy (at least on the second level). What it does is make the stealth aspect more fast paced but the upgraded version is just for the sake of having it. There might be scenarios where you can engage a small group of guards and they don't alert anyone, kill them off and you have less enemies to worry about.
Bone Charms are a total of 45 in the game. You can unlock a max of 10 individual slots to place the charms you've found. According to Bethesda there are 12 bone charms you can find in a playthrough that are randomized out of all the 45 that exist. You can upgrade/equip abilities as well as bone charms even during a mission.