Since you don't battle the queen in her human state for the last battle I feel it is safe to leave that sprite out since it is already shown in another location.
The animated map for the Inside Lavos area would be kewl. I will wait for BizHawk to be ready before I take that on. zSNES with vSNES is not very user friendly for capturing many frames of animation. I have not made an APNG yet. Is that supported by the major browsers at this point?
The Flyby 1 does have the ship, however it is all at a weird perspective that would not match the top down view of the map. In the 2nd flyby they actually show the sprite with the top down map view so that is why I included it in the 2nd flyby and not the first.
Let me know what ending Crono and Marle flying off together is from. What I need to do to get it, or provide a Save State File just before that ending.
Black Omen:
The normal queen sprite also appears on the last Black Omen fight screen, maybe include that? And maybe put the enemies in both elevators into them.
Inside Lavos:
What's the policy on animated GIFs/APNGs? It seems this page could utilize them...
Ending Flyby 1:
The ship also appears on that screen... Anyway, there's an ending where Crono & Marle fly into the sky, maybe include that sprite?