Well, I got used to this new scrolling after like 5 minutes so it's no big deal.
In my opinion though, scrolling on Lion is less intuitive because you're not directly touching the page, but a trackpad. On the iPad you are, that's why it's natural there.
Give it time! I got used to it with Scroll Reverser in Snow Leopard. It takes a day or two to get used to, but when everything you touch has natural scrolling in a few years, your Mac is going to feel awkward if you still use conventional scrolling.
I thought WTF when I started using it during the beta, but after a week I use to it and when I switched back to my SL I was confused. It grows on you unless you switch between non Lion computers a lot.