Colorado Rockies, Western Slope canyons, and Donner Pass over the Sierra are magnificent any time of year. It won't be barren (the barren parts are in western Utah and Nevada at night). Even the desert west of Grand Junction is good, doesn't look much different any time of year and the Book Cliffs are visible north of the tracks all along that stretch.
In Emeryville, the Hyatt is most convenient, right across the tracks from the station and accessible by a pedestrian overpass. Not sure of the price but the location cannot be beat. Am not that familiar with Chicago, someone else needs to weigh in there.
As to the 14-2 connection, don't worry about that too much. The fact that Amtrak maintains the guarantee despite the less than 60 minute connection now says something. Amtrak is loathe to lay people over 2 or 3 days for the next Sunset/Eagle, and almost never gets in a position that they have to do it. Some form of connection is almost always made, plus the Starlight has like a 30 minute pad going into LA and runs detrain only from Santa Barbara on, so doesn't have to "hold for time" at any of the stops south of there into LA. I've been as early as 8:25 pm into LA on it. However, it is always not always done by holding the train, or at least holding it very long. The following methods are used on to protect that connection.
1. If a delay is encountered south of the Sacramento so the connection will not be made, Amtrak will take Sunset/Eagle passengers off the train at Oxnard and bus them to meet the Sunset/Eagle at Ontario or Palm Springs. The bus can make that much faster than the train (the bus won't even go through downtown LA, but passes north via Pasadena on the 134 and the 210).
2. If a delay is encountered north of the Bay Area, such that the connection cannot be reasonably made (it would be a pretty severe delay) Sunset/Eagle passengers are re-routed onto the much faster San Joaquin/Thruway bus connection to Los Angeles. Since you are at Emeryville, you would be just reticketed from there. Passengers already onboard are generally taken off at Sacramento, Martinez or Emeryville, usually Sacramento. If that is the case, which is thankfully rare these days, you'll miss the coast run on the Starlight, but you will make the Sunset/Eagle.
To further assuage your concerns, from Sacramento south you should not experience much freight congestion. The "Cal-P" between Sacramento and Emeryville is largely a passenger railroad these days, CalTrans has elected to pay far above Amtrak rates for its Capitol Corridor and San Joaquin trains and UP has diverted most of their freight traffic off the line. South of San Jose, the UP Coast Line has very little freight traffic, no through freight at all, only some locals. Most of the rail traffic from San Luis Obispo south are Pacific Surfliners, not freight trains. The only real dispatching issue is from Camarillo on into LA is that stretch is owned and dispatched by SCRRA (Metrolink) and they favor their commuter trains but that really isn't a big deal.
That is a quite a good fare for 4 roomettes, Eagle/Zephyr/Starlight/Eagle, congratulations. You couldn't get much, if any, lower.
