Awesome! I am a big fan of RPGs - so much so that I have built an RPG pinball as well (Quest for Glory - which has a thread here on Pinside if you'd like to see some of the ideas and how I handled their implementation. Many things you've mentioned are quite different and more traditional than my approach, but I suspect that many things will be very similar).

In my project, I included a couple of small multiball rewards as you progress through the game. These are a nice reward or surprise, but including in the general flow of my game did not work. My opinion is that changing commonly accepted features is fine if it's what you prefer or if it matches the expectations of the player based on the game flow.

Best of luck on your project!