The palettes could use some improvement.
Regarding the alien ship colours, the ramp going from yellow to green to orange looks rather odd, because hue values go back and forth considerably in the asteroid ramp.
The human ships use a lot of grey, which tends to look boring. The red and orange are nearly identical.
Here are some palette edits:
For the alien ship I used the green from the original and made a new ramp from there.
I also gave the greys a blue hue and made the lightest colour in the ramp a bit lighter.
Also, some ideas for the ships themselves:
I think it would be better if the bubble exhausts on the alien ship went a bit more backward, to show more clearly where the ship is heading. I also shaped it more like a cone for the same reason.
The many lines on the round ships, as well as the other ships make conveying depth difficult, and if the sprites are going to rotate the lines won't be readable in most directions. The edit hopefully shows more depth.
On the whisk/scanner I didn't change much, but simplified it a bit. The thick outlines on the original make it hard to read.
For the double-barreled ship I did the same as with the round one, and added an idea for some firing effects.
Any other edits are mostly personal preference. Good luck with the project!