I am excited to find this. Picross is pretty much the only game I play on steam anymore and this is a definite improvement. I had an idea to do this, but I think your way is better than what I was imagining.
It needs a "Next Level" button on the completion screen.
There is some buggyness in the functionality of the X marks. When I added some Xs in color #2 mode, I couldn't remove them by just clicking them again. I went back into both-colors mode and reset those tiles and that cleared the Xs.
I agree with YeahEsCereal, a brief tutorial screen would help. All it really needs to point out is what the numbers on different sides of the board mean. It stumped me for a moment.
I see you've said there will be no further updates, but if you do take another whack at it, I suggest these things:
The way the Xs are handled needs to be re-thought. I think I'd be nice if Xs change colors just like the filled tiles do, and if an X of one color can add onto a filled tile of a different color.
Remove the exclusive color modes. I felt like the fun died when I found that. The challenge was more fun trying to fill in all three colors together.
For the simple little thing that it is, this is great, thanks for making it. I had fun.