Yes, there will be a small upgrade fee for MA3.
"Lifetime" upgrades are an urban myth. What I said was that some upgrades would be free (there were many), and some would not. My original plan was to make the 3D background free, then charge for extra fish. That was when I was the only person involved. Since then, publishers, distributors, store chains, etc., have become involved and now there are dozens of families to feed. I hear that Micosoft will also be charging to upgrade from Vista to Windows 7