I want to create a story-like game which depends on situations based on your decisions. I don't want to have "battle scenes" in my game; can I disregard the EXP/HP stuffs to create my own game?
Yes, you can. I have made a few games like this; you may even be surprised to learn that RPG Maker can be used to make non-RPG games; see this blog post on the RPG Maker blog.
Games people have made include:
- Interactive fiction
It's really up to you whether you use (or don't use) aspects of the game.
Also, due to the (insane) level of customization, you can also get away with things like disabling/removing menu items (if they're not used for your game).