Maybe portions of the old alignment could have Historic US 99 signs erected. That seems more likely to me than the CA 99 corridor between Mettler and Sacramento becoming an Interstate Highway.
My personal opinion is 6 lanes minimum between Wheeler Ridge and Sacramento is the way to go. If that somehow accomplishes Interstate standards great...if not the improvements will be welcome. Sparker has a lot more information on the long term future of 99, it seems at some point the corridor is destined for Interstate status.
Regarding US 99 there are segments that could be signed as historic routes but much of the alignment was built over by the current freeway. Bakersfield has essentially intact historical alignments and believe Sacramento does as well. Fresno has butchered up Broadway too much to make a Historic alignment outside of Golden State Boulevard not very viable.
The current Caltrans "master plan" for CA 99 calls for a minimum 6 lanes overall, with some 8-lane segments around Bakersfield, Fresno, and in the Modesto-Stockton area. And Max is correct; many of the original US 99 alignments in the smaller towns were directly overlaid with freeway from the '50's on; however the larger towns: Bakersfield, Delano, Tulare, the stretch from Kingsburg north into central Fresno, parts of Fresno itself, Madera, Merced/Atwater, Turlock, Modesto, Stockton, Lodi, and Galt all have viable segments of the original road that could lend themselves to historical signage -- besides functioning as virtual business loops in the process. In Fresno, the part through downtown
has, as Max avers, been chopped into segments; north of downtown and through the traffic circle near Roebling Park there is still a functioning "old highway" that could be utilized -- signing downtown would require a system of "bridging trailblazers" to get interested folks from one actual existing segment to the next.
A historical route through Sacramento would be fun inasmuch as there are several alignments to select depending upon timeframe. Personally, I'd stick with the first -- straight up Stockton Blvd. to Alhambra, then north to "L" Street, and west to the northeast corner of the state capitol grounds at 15th Street.
I had an idea that I posited some time ago -- if and when CA 99 becomes Interstate 7 or, more likely, 9, the whole thing from Wheeler Ridge to Sacramento could be co-signed with the usual rectangular beige signs as "Historic US 99" -- but the difference would be that the historic route would depart the freeway through the larger towns with viable original alignment to serve as a business loop through each. IMO, the (arguably) 2nd most important westward-migration route in the country -- and often the last leg of such a journey -- deserves at least as much.