Well, that's actually due to a mix of factors, but yes, I'm certainly aware of the problems. I tried out Ren'py before starting this project, but it just didn't seem to be a great choice. In the early stages of developing PAT I found VNM was giving much better results, as well as being a lot quicker to work with. Back then they were also actively patching the engine, too, so it seemed like any issues were going to be dealt with. Had I known about these issues in advance I probably would have preferred to try getting into Unity right from the start, but at least working in VNM has been a learning experience for me, as it's much more like Unity than anything else I'd used before. (Adrift, mostly.)
I've taken a quick look at Unity's Naninovel plugin and it seems pretty neat; it also has a much more active developer and Unity comes with a wider community, so it will hopefully be easier to fix bugs and that kind of thing. It also has a lot of in-built functionality for presentation and stuff. It'll still take a while for me to figure out how to use it well, though, particularly when I need to keep working on other things too, but I'm getting a start.
