My goal would be to utilize big cities you already have, and use those to connect to the other bigger cities that aren't seen passenger rail as of right now. I'd do these:
-Chicago -> Indianapolis -> Louisville -> Nashville -> Atlanta -> Macon -> Jacksonville
Daily. Have a good number of smaller stops in between, of course. With that, build a brand new big 'Union Station' in Atlanta. Maybe a crew change in Atlanta too. I'm split whether to run Superliners along this route or do what the Crescent does (which I'm leaning towards more). For the southern part, utilize the portions that they're about to make into the Atlanta to Macon route. There's just that huge "gap" in the routes right there (look at the map and see what I mean).
http://www.saveamtrak.org/floridia_rg_map.jpg
This would restore part of the Floridian, except moving it east. It'd be nice to somehow work in Valdosta too though.
-New Orleans -> Mobile -> Pensacola -> Tallahassee -> Jacksonville
Restore that old portion of the Sunset Limited. Leave in the afternoon and arrive in the morning. Same consist the Crescent uses.
-Jacksonville -> Ocala -> Dade City -> Tampa -> St. Petersburg -> Sarasota -> Ft. Myers -> Miami
Get some service on the eastern side of Florida. Same consist the Silver Meteor uses.
-Extend the Heartland Flyer and make it truly "Heartland".
Ft. Worth -> Oklahoma City -> Tulsa -> Kansas City -> Omaha -> Sioux City (or Sioux Falls) -> Rapid City -> Casper -> Boise -> Portland
That seems a bit long though. Maybe it can be broken up into 2 but I think it'd be worth it if it was just 1. It seems longer than the Zephyr route, but can't be worse than the SW Chief. Load it up with Superliners of course. This would restore portions of The Pioneer, but cut out Salt Lake City.
-Los Angeles -> Salt Lake City. Restore the Desert Wind route. Maybe make it go to Minneapolis? Hard to figure out what to do with it after SLC. It'd be nice if it was long distance though.