You're absolutely right. In fact, after I went through all that stuff if my previous explanation I ended up getting rid of the shrine system completely, making the whole leveling system more streamlined and easy to understand so that it would be easier to focus on more important things.

The reason I haven't mentioned much of the plot is that the whole thing is really still in its early stages and I still have some holes to fill. Make no mistake, though. A good plot and emphasis on character/setting development is very important to me. Posting this here has already made me aware of many of the faults I need to focus on.