I am a 3D modeller so probably 3D, but I prefer the 2D look for these games. I'll use simple 3D objects during development and finish in 2D with an artist friend, but I haven't even started yet so that's neither here nor there at the moment.
As for C or LUA I'm not sure. Like I said I'm new to the programming side and that's why I came here to ask. I'm not sure which will be better for me as I have to learn from the ground up. I understand that learning while trying to develop a game will be difficult and arduous, but I'm up to the task.