1) It would be largely filmed on green screens and partial sets. The city would be accomplished through use of large scale miniatures (aka "Bigatures" as Weta calls them), perhaps superimposed onto real geographical locations.
2) The location would no longer be Tokyo 3. I'm not sure I'd want to move the story to an American city like LA, but I might. At the least I'd probably move it to a Mediterranean country like Turkey, and have "Neo City" set up by the UN in the wake of the world's costal cities being flooded, which means that the political scene would be fairly unusual, and it would essentially be a hodgepodge of various cultures from around the world converging into one economic nucleus.
3) The Evangelions would be CG. I'm not going to try and kid myself into thinking that they could pull them off convincingly with lanky contortionists in costumes or animatronics. Maybe there'd be one full-scale model of Unit 01's head and / or feet for the actors to interact with on set, but that would be pretty much all in terms of physical Evangelions. Every other time you see the Evas they would be CG (as in, 90% of when you see them), since we easily have the technology to make them look convincing.
4) I know that this isn't a terribly popular opinion amongst fans, but I'd make the pilots slightly older (15-going-on-16-ish) and cast 18-25 year old actors. I've explained my reasons before, but to sum up, it would remove the hassles involved with working with child actors, better selection pool, and less controversy around the plug suits. Also, no problems with

5) Hugh Laurie as Gendo. 'nuff said.
6) I'd do it as a trilogy. First movie would introduce the characters (including Asuka, unlike Rebuild), the second would explore their relationships and end with Shinji being absorbed into Unit 01, and the third would feature Shinji's return, the characters being depressed, third impact. I'm not sure how much it would divert from the source in terms of how the last movie plays out. Maybe after I see the rest of the Rebuilds I'll have a better idea of how I'd like it to end, but for now we'll say it would be similar to the show's ending except much more condensed, and with a bit more resolution.