Instead of having the guide-line appear randomly, give the player some resource that increases in some way and that decreases when he wants to summon the line.
Also, the penalty system is not clear. Sometimes after the new balls appear the "missed shot" bar doesn't fill up completely.
It's really hard to figure out the rules from the examples. Is this part of the puzzle? :-)
My take on the rules:
1. Only the colors of the direct neighbours matter.
2. There must be at least two atoms with the same color among the direct neighbours. These atoms are completely eleminated.
3. However, a single atom may be unmatched. This atom is left over.
4. The central atom doesn't matter at all, at always vanishes.
Nice game otherwise.
 "Bubble Sky")
 "loops of zen")
 "Bush Whacker 2")
 "NoNoSparks: The Ark")
 "Atomic Puzzle 2")