Well, Neon, you give quite the complicated ideas. I'll tell you what I've been currently thinking.
There are 3 different... let's call them skills. Element magic, close combat, ranged combat.
For each skill, there are 4 different powers. Powers decide what your normal attack, defense, spell and perhaps other stuff are.
Normal attacks take no MP, but aren't all that strong. While defending, you take less damage and regain more MP. Spells are powerful, but also take MP.
You start by choosing a skill and a power from it. During the game, you can eventually learn the other 3 powers from it.
If you have three powers, for example, then you can use the attacks, defenses and spells of each separate one, of two of them combined, or of all three of them combined.
So there's a total of 45 different attacks, defenses and spells. During a game you can learn 15 different.
I haven't however thought of what all of those are and what they do. Three quarters of the time I'm making this, goes into thinking up what to make, not making it.
So I'll take some of your ideas into thought and probably use them. =)
GlyphGryph, I know that sounds real interesting and deep and such. But, like I said, it's conflicting with the other ideas and would be really difficult to make. I'm sorry everyone, but don't keep offering it. I'll make a house as your home, where you can do different stuff or something...
Also, seems like there was some confusion. You play as the supervillain, not the superhero.
I was also slightly amazed that not one person suggested me not making a game and some... I don't know... simulation or thingy instead. (I did offer to make multiple programs simultaneously.)