One thing I’d love to see is the ability to toggle the continue prompt arrow, and insert it into the dialogue box (as done in-game). You know, the little arrow that shows up in-line or at the edge of the box when you’re supposed to press a button to advance the text.

That said, I’m also going to need a second tool to actually create scenes for use with this one. Any recommendations?

We've got something in mind for the "advance" button in the future! Besides from that, it's best to use an image editor to make scenes! I reccomend using sprites from Skytemple, PMDCollab's sprite repository and the Spriters Resource. You can use any program to edit the image, though i'd reccomend aseprite, pixel studio or any capable art program.