I think we should stick to 640x480 as default. Why? There are already many RMXP resources in that resolution.
I first wanted to go with 800x600 as well, but as I said, this is probably the better way to go. Also, I don't have the original PSD anymore for the screens I have added to the RTP so basically I can't remake a high quality image in a higher resolution. The only thing I can do is resize it manually and that will look ugly.