It's wrenching as it is, and I think it ought to stay that way.
I don't mean the earth movers and the exposed parking decks and roadbed. I mean an enormous hole in the ground, so wide and so deep it makes you shudder for a moment (3).
I envision a park on the site, at the bottom of the seven-story pit. The walls are surfaced with rough granite, in which the names of those who died are carved, and over which ivy will eventually grow (4). The footprints of the two towers are reflecting pools; next to each stands a single spire, designed to look like the ornamental facade of the lower floors of the towers. You could fit a small and quiet museum in there, too.
All these details are inconsequential. What matters is the preservation of the hole, the symbolic emptiness. Better than new high-rises or a shopping mall. It's the chance to rework a void into a place of peace and beauty and life. First you experience the gap; then you notice that it is green and alive, that life continues even in the presence of great loss.
(1) Conventional usage has assigned this place a capitalized proper name -- G Z -- but I refuse to use it.
First, the term is aggrandizing, exceptionalistic. Lots of tragedies have Gs Z, but Americans have appropriated a generic military term and applied it to the entire site on which the World Trade Center formerly stood, in much the same way that another generic military term became the standard name for a particular amphibious invasion in northern France. Picking one unique referent implicitly denigrates all others (and besides, if I had to pick just one, I'd pick Hiroshima).
Second, it's sloppy language. Pictures of Gs Z typically show destruction, raw earth, smouldering fires. By back-propagation, the term gets applied to anythihg matching that description. But the phrase is more precise than that; my dictionary refers specifically to a nuclear weapon in its definition. Sloppy language leads to sloppy thinking; look at how any conversation about "terrorism" seems inevitably to end up stuck fast in a semantic tarpit.
And third, it's dehumanizing. I've come almost to like the use of "9 11" and "September Eleventh" as metonyms  for the events of that awful day. They're evasive, but they wear their evasiveness so openly that they obscure nothing by it. And because they're empty shells, without preexisting semantic implications, they've come to carry exactly the emotional freight that we've been pouring into them. Not like G* Z*, which is sterile and militarized. Trying to speaking movingly about G Z is like speaking erotically about the retroglandular sulcus or the urogenital diaphragm: you can do it if you're serious about it, but your words are working against you.
(2) Look it up! I did, and I learned several neat things from the experience.
(3) The hole was never anyone's intent, which may be why I think it works. Something this tragic defies direct thought; you have to back your way into contemplating it.
(4) A quick back-of-the-envelope calculation suggests that there would be about ten square meters per name. Not enough that the names will all be legible from everywhere on the site, but enough to make them startlingly massive and enduring.