Maybe killing off the creature is too much, now that you mention it. How about changes the element of the creature and does five damage if its dark.
Eclipse: +3/+2. Correct me if I'm wrong.
Improved Core: +0/+2 for Fire, +2/+0 for Earth, -1/-1 for Life, and costs more. Doesn't seem that broken to me.
Flood - The idea is that it could be a great card situationally (against mono-fire), but otherwise would most likely not help at all. It would be like protect artifact in god farming decks. Sure, it would help against seism, but against all other decks it would do practically nothing, and may even help the opponent.
Forest fire - The idea is to be a mass deflagration of life cards. I worded it wrong in my post; it was supposed to have the same effect for everyone.
Darken/Angelify - I'll take out the auto kill.
Quantum Shift WOULD only hurt Rainbow decks severely. I just don't think you understand its effect.
Let's say I have a Rainbow deck, middle-end game. I have 10+ quantum in every single element, and am thinking I'll win. Then the opponent plays Quantum Shift. A random element is chosen from a pool of all the elements I have, in this case lets say Dark gets chosen. ALL of my quantum are transferred to dark, so I now have 120+ Dark quantum and 0 other quantum.
Now let's say I have a dual deck, Air-Life. I'm running an FFQ deck and have all the queens I need out. I have 2 life quantum and 30 air quantum, and need more life to make more fireflies. Luckily for me, my opponent is stupid and plays Quantum Shift. A random element is chosen from the elements I have (so either Life or Air). Life gets chosen. All the quantum gets changed to life quantum, so I now have 32 life quantum and 0 air quantum.
Now let's say I have a mono deck, Fire, with 40 quantum. The opponent plays Quantum Shift, and it chooses the only element I have some in, fire (duh). Since I only have fire and all quantum I have are made in to fire, it has no effect. I still have 40 fire quantum.