Fun fact: The official reason given by takashi iizuka (the Sonic Adventure's director) as to why beta windy valley was scrapped was apparently due to the dev team running into to many deadlines to include this level as intended, so it was redesigned so that they could ship the game on time. As it turns out, the final version was one of the last levels to be completed.
Oh wow, that's interesting! There are a few redeeming factors to the new version like the wind running and the tornado section but that original version looked like an entirely different game!
So a little I wanted to add about Sonic being the ultimate life form. Shadow was designed based on the prophecy that would later be the final boss battle between Sonic and Perfect Chaos. Biolizard is a prototype because it was designed based off Perfect Choas but Gerald Robotnik realized he should instead copy from the Hedgehog. Shadow quills go up because Super Sonic quills go up and he inherently has the ability to use chaos control because he was designed from the ground up with the chaos emerald energy in mind, because that is what powers Super Sonic. Somewhere in the game I think maybe only in the Dreamcast version but not sure, you can find hieroglyphs of the Sonic vs Perfect Chaos prophecy. So yes Sonic is the Ultimate life form, Super Sonic that is. Sorry I just had to add all that. It really makes SA2 feel like a sequel.
Don't be sorry. I love the deep implications that are involved in Sonic lore as it makes the world MUCH MUCH cooler. You're right, it DOES make SA2 feel like a sequel as the Chaos/Ultimate Lifeform comes full circle, that's actually so awesome!