Okay first off I LOVED it! Telltale has done a great job of outdoing themselves every season.
But some of the stuff near the end confused me. Strangely enough this isn't the whole alternate Max thing, it more has to do with the other characters.
First off, what happened to Grandpa Stinky? Did they ever restore his brain (I know they saved Flint from killing him but does he go back to normal?)
Second, who calls Stinky's cellphone at the end? Initially I thought it was Max using his psychic abilities (as kind of hinted by when you see something twinkle in the sky and Sam says "Max?"). I figured he actually survived by teleporting to Skunkape's ship until the alternate version showed up at the end. And another thing that confused me was did Skunkape's ship explode and if so did Girl Stinky and him both die?
I loved the game but the ending left so many loose ends! Hopefully these'll be explained when the inevitable season 4 comes out in a year or so. :)