I confess I love your idea

I love interlocking organic moving ships with gross animations

and I fancied your ship design.
Here's a suggestion:

- Try to play with each frame's timing, not every frame has to be on screen for the same time duration. You can get more interesting results by playing with this. (Also, duplicated one of the initial frames, added it to the end, so it loops a bit better).
- Your palette becomes much richer if you don't just use linear color gradations - as in keeping the color's hue and only changing the value. You can risk large hue changes between different colors on small graphics, such as yours.
On your version, i think the colors where too saturated, and too distinct from each other's - the pink area too different from the green one. Usually, the colors of and object will share some properties, even if the materials it's composed of are largely different, due to the illumination being the same, light reflected by the ambience, etc.
On my edit, i tried to play with the palette so that there was some unification amongst the greens and the pinks. Also, i played with each of the tones (each tone, from the highlights to the dark tones) to make the colors more appealing, contrast better with each other (if i suceeded, that's a whole other story).
edit: now that i look at my edit, i don't like the palette that much... but the tips still hold