[Florian Claaßen]

Is it correct that you use a cutout, so only a part of certain frames for the animation? If so, I wouldn’t recommend that given your circumstances, because that would mean that you’re practically wasting the memory storage (which is already limited). What you could do would be to animate your sequences in After Effects and then export the animation as a png sequence with heavy compression.
This would safe you a lot of time if you were practically animating the frames in the ROM itself prior, and you might even get smaller files.
Considering that you’re modding (or rom-hacking if that’s a word) an old game, you would easily get away with very low-bit frames, so maybe limiting the color space to a low standard, perhaps even 8 or 16 bit could do you another favor memory-wise.