...he'd jettison the shots that call for Avner gazing forlornly at the model kitchen display, which is supposed to signify the sensitive Mossad assassin's anguish at being forced to choose between the duty and family (or rather, the Motherland and the Mother of his child).
...he might tell Tony Kushner to figure out a way to write a convincing reason for Avner to take the agonizing job in the first place -- besides providing some vague allusion to living up to an Absent Father.
...he likely would've shot the film in the same jittery, quicksilver style (lots of quick pans and jump cuts) with a desaturated color scheme as the actual Spielberg film (one of the best things about the movie), akin to his 70s-era-styled thriller Traffic.
...his cinematographer "Peter Andrews," though, would likely have avoided some of those interior shots with the Storaro-type high-contrast lighting schemes (scenes of Avner brooding in the shadows, backlit) that, in a film shot in a flat, documentarian style, sticks out like a Kandinsky at a Pre-Raphaelites exhibition.
...he also certainly would not have felt the need to reprise the "Girl in Red" scene from Schindler's List.
...would Chopper-Man burst into tears upon hearing his baby cry?
...he would likely have retained what works like gangbusters in the screenplay -- the riveting set-up, the foolproof subject matter, and the scenes between Avner and the mysterious Frenchies.
...he would likely have retained the screenplay's rather wishy-washy humanistic perspective which, as it so happens, is the correct moral stance on counterterrorism (essentially, counterterrorism perpetuates a cycle of vengeance and robs the avenging angels of their humanity, but hey, you've got a better solution?).
...he probably couldn't do much with the screenplay's central problem, which settles on variations of the following formula: meet source, find target, stake out target, almost botch killing target, kill target, Avner looking traumatized, the group discusses the morality of the assignment, Avner expressing doubts, Avner assuages doubts and continues, wash, rinse, repeat.
...unlike the film's actual director, he wouldn't feel compelled to continue the six or seven movie streak of marring a film with a scene so wildly misjudged, so embarrassingly maudlin, that you begin to wonder if Spielberg isn't routinely allowing Chris Columbus to ghost-direct three days a shoot while he tends to Dreamworks' troubled finances. Here, it's Avner orgasming to the flashback of the airport massacre, a cross-cutting folly that must be seen to be believed. (It's easily the worst sex scene in the movies since Marc Forster threw in random flash-inserts of P. Diddy as Billy Bob and Halle gets it on behind an obtrusive birdcage.)
...and most importantly, unlike the film's actual director, he'd realize that a movie about the central political issue of our time is not the place to indulge in yet another pointless iteration of the Absent Father/Must Be a Good Father theme.