Yeah, Pyxel Edit is great for tiling, but I like Aseprite for animations and because it's super fast and easy to use. I get a lot of use out of both actually. But yeah, it's tricky to do stuff like the water tiles without Pyxel Edit.
Puzzle and Movement
Battle System 0.01
[Update] The groundwork for the battle system is done, though a decent amount of work still needs to be done. The last big thing I need to make is a simple dialogue/scene engine and then I can really start building more on the game. I also finalized the resolution (NES Res now instead of widescreen) and started settling on a graphical style.