Actually what they proposed was keeping both foot prints clear, and building one tower with the ground zero boundry and one on the site of the Deutsche Bank building south of Liberty Street. Preserving one footprint is an interesting idea but I suspect both foorprints will be remain clear except for memorial space.
After second glances I think Zapata's scheme has some attractive qualities, but I think it's scuplural ala Frank Gehry for the sake of being 'look at me' architecture. Not completely appropriate for the site. I happen to like the memorial promenade with the water but I wonder how that could be achieved with a highway below it. I also think that the tower is too massive for the site. There also seems to be too much fragmentation between the tower and the complex of buildings at the base.
That being said, it certainly is one of the more sensitive schemes I have seen. As is the Pedersen scheme. However I believe both are fatally flawed.