Secret Elements:
Lava: Not secret, but it is difficult to place. You need to turn temperature on, then place stone in an area with extreme temperatures. One way to do this is to use multi to clone gas, then ignite it. Another way is to use a heater. Replacing another element with lava usually works.
Mud: Add water to soil.
Plants(Stem, Petal, Pollen): Add seed to mud.
Ash: Burn seed, fish, or ant by rasing them to a high temperature.
Quicksand: Add water to sand.
Glass: Raise sand to a high temperature.
Snow: Cool steam to a low temperature.
Tunnel: Add an ant to soil. It will start to create tunnel around its path.
Heated Oil: Heat oil.
Acid Rain: I have no idea.
Graphics: Yes, I know they are bad, but they are a lot better then they were in the original game. Everything in the original game was the same shade of gray and the spites were an oval, a square, and a square minus a parabola.
2p Mode: I'm not sure how to implement a co-op mode, but I could defiantly make a vs mode in the future.