To be honest, I am actually rather impressed, that for a new person to rpg makers, you havn't gone for the old fashioned, cliche plots.
The plot you do have seems to be very interesting, and I look forward to seeing how it unfolds. I hope you can pull it off and create an enjoyable game because of it.
As for the RTP, I've never minded it. If you can learn what your doing, it's plain old simple and nice to use. Obviously, the odd non-RTP thing does make the player go 'oo-er' (In a good way!) but you worry about that after you have got better at more important stuff, like mapping, creating a good story and eventing. It could be useful for you to insert some scripts from the scripts database that you find interesting however, as the base interface (especially for the battles) can be boring for some. Again, you shouldn't need to worry much about these till later in the development.
To do with help I can offer; I am good at Eventing and pretty damn good at mapping
. If you would like help in these areas, don't hesitate to ask. I won't be making the maps for you as such, just showing you what to do to get the map you desire (If you get what I mean..!).
I hope your project goes well,
~Darico