You can add multiple Input nodes and connect them to nodes that aren't in a chain, so you can apply different effects to different layers. The node system will have a major upgrade in the following updates though.
The GIF support is kinda there, I need to improve the support and performance in a future update too.
Palette customization sounds great, but that would probably take a huge chunk of development time that is more needed in other places at the moment. I've added it to the private roadmap so It's something that I'll tackle at some point in the future.