Thank you!
I was doing each character seperately sort've, mostly worrying about making them readable from the environment. It didn't occur to me that hue shifting each of them to their own colors would end up making them feel like they don't belong together. It occurs to me now!
Also, as a side note, how can you see this if it hasn't been approved yet? I'm sorry I am new to this site >.>
Edit: I changed it based on what you said and posted here. The contrast feels weird now, although I'm not sure how to fix it.
I'm not familiar with Krita's animations tools (tbh I didn't even know it had animation tools) so I'm afraid I can't help. It's possible that ffmpeg, not being designed for pixel art, gets confused with the colours in the transparency (just because you can't see them doesn't mean the data's not there) and when it reduces the palette, it does it wrong. It's also possible it does some other weird stuff in the encoding - maybe not even due to ffmpeg itself, but due to how krita interfaces with it.
Anyway, more on topic, a few critiques for your image:
The sides of the brick blocks are mirrored instead of having long and short sides to the brcks, the mirroring is very obvious and the bricks make no sense as a result.
The sprites look nice! The base is a little weird, but with clothing and hair added, they look just fine.
I think the colours look a little all over the place. You're hue-shifting, but you're hue-shifting each ramp in a different direction, so the colours have no unity. Pick a single "ambient colour" and hue-shift your ramps towards that hue. That'll help all the colours feel like they exist together in the same scene.
That site worked, thank you *c* Although I realized after I did it that I used the background color for the archers sleeves. Oh well.
And I don't use export, I use ffmpeg with the 'render animation' option. Exporting it as a gif just makes a .gif file that doesn't move. Krita can be a little odd.
You can use this online tool to replace a specific colour with transparency. Weird that Krita messes it up though o_o; Do you make your image indexed before exporting? If not, try doing that and exporting with it already indexed.
It is good. i think the problem is the head / face direction.