The crux of the matter:
1) Will Lion change the software install policy to App Store only (like iOS)
2) Will the App Store create an un-level playing field years from now by training users to only install Apple certified software.
2) Will the App Store create an un-level playing field years from now by training users to only install Apple certified software.
No, unless you think Autodesk wants to give Apple 30% of the $4000 price of AutoCAD for Mac on each sale.
2: It could, depending on how Apple implements and pushes their App Store.