OK, so in regards to the first YouTube link you posted. All in the first level: The Genesis colors definitely look less vibrant to me than the SNES version. The HUD is duller and has less colors than in the Genesis version. Look at the leaves on the trees throughout the first level, they're darker in the Genesis version and more vibrant on the SNES. And look at the background during the Rufio fight at the end of the first level (6:48 is a good still frame). The background is darker, the log that they're on looks way less vibrant. Rufio himself might seem more vibrant, but this is actually not a good thing. In the Genesis version he has light blue clothes, but in the SNES he has black clothes (like he does in the movie). Look at the water that you swim through toward the beginning of the first level, it's proper translucent in the SNES but dithering fake transparency in the Genesis version. Also note that in the SNES version once Pan reaches Tink and flies to the next part of the stage it changes to winter then briefly autumn then back into spring/summer (which mimics a the movie). The season change is completely missing in the Genesis version. The Genesis version is also missing the rain that can randomly pass through in the SNES version. At the end of each level, in the SNES version the screen dims (minus the HUD) and the score is overlayed on top of it. On the Genesis version at the end of the level the screen goes black (still with the HUD remaining) for the score tally.
14:03 is another good still frame to look at (still the first link). Again, the water is proper translucent on the SNES, and you can see the clouds through the water on the Genesis. The clouds themselves look better on the SNES than they do on the Genesis. The sky color might be a brighter shade of blue on the Genesis, but I think it looks better on hte SNES. More natural, like a real sky color and not a cartoon representation of sky, and the clouds definitely help to make it look like a more natural sky. Then 14:05, look at the cherries, definitely more vibrant on the SNES. Then let it play just a few seconds more and look at the boss fight. I think the colors of the boss sprite on the SNES looks better. When you hit the boss on the SNES version the sprite flashes. On the Genesis when you hit the boss the background flashes but not the boss sprite. Which thing flashes might be a whatever kind of thing, but it seems like the sprite should flash and not that background. Maybe this was a limitation of the Genesis hardware when it was ported? Don't know why else they would change it.
As for the music, it definitely sounds better with the SNES' sampling than the Genesis chip tunes. Maybe it comes down to which sound chip you prefer, but I bet if you had a non-90's gamer listen to both they would say the SNES sounds better. I think the Genesis version might be missing certain parts in the music too. And I guess there's not enough channels because it looks like a track will mute to play a sound effect at times.
edit: I just spotted checked the music from the third link and the Genesis version is definitely inferior to the SNES version. I think they got lazy when the ported it or had a tight schedule to do it in, but some of the tunes aren't arranged the same way. And it's not just a preference to which sound chip you fancy, the SNES version is better. It has a sweeping orchestral feeling to it that the Genesis sound chip (even as bad ass as it is) cannot replicate.
Anyway, now that you got the gist of the game with the SNES and Genesis versions, check out the Sega CD version and tell me I'm not crazy. Clearly they were like "Oh, it's on CD so lets do movie score, voice overs and FMV" but didn't really care how it fit in there. So they got some crappy FMVs, horrible voice acting, and shoved the movie score in where it didn't belong.
https://www.youtube.com/watch?v=VPgMcP3sY2Y
