Now I haven't ridden the EX Milwaukee Road, or the EX Northern Pacific but I will join this discussion anyway.
Of your five routes from the midwest to the Northwest each had their own merit.
I'll grade the trains on each scenery, equipment, food, and schedule. For starters here is a list of routes.
1. North Coast Limited (Burlington Route Chicago, IL-St. Paul, MN, Northern Pacific St. Paul, MN-Seattle, WA, Spokane, Portland, & Seattle Pasco-Portland) via St. Paul, MN, Fargo, ND, Bismark, ND, Billings, MT, Butte, MT, Spokane, WA, Pasco, WA.
2. Empire Builder (Burlington Route Chicago, IL-St. Paul, MN, Great Northern St. Paul, MN-Seattle, WA, Spokane, Portland, & Seattle Spokane-Portland) via St. Paul, MN, Fargo, ND, Minot, ND, Whitefish, MT, Spokane, WA.
3. Olympian Hiawatha (Milwaukee Road Chicago, IL-Tacoma, WA) via Milwaukee, WI, St. Paul, MN, Aberdeen, SD, Butte, MT, Spokane, WA, Seattle, WA.
4. City of Portland (Chicago & Northwestern/Milwaukee Road Chicago, IL-Omaha, NE, Union Pacific Omaha, NE-Portland, OR) via Omaha, Cheyanne, WY, Boise, ID.
5. Mountaineer (Soo Line St. Paul, MN-Portal, ND, Canadian Pacific North Portal, MB-Vancouver, BC) via Minot, ND, Moose Jaw, SK, Calgary, AB, Kamloops, BC.
From now on I'll list them in order of best to worst.
Scenery:
1/2: North Coast Limited. Going westbound you cruise along ole man river for 300 miles in daylight. Cross over North Dakota overnight, and enter the Rockies around noon and stay in them the rest of the day. They had a beautiful route across Montana. Fun fact the secondary train the "Mainstreeter" used a different route and went via Helena. Equally scenic.
1/2: Mountaineer. Nothing really can top the remarkable beauty of the Canadian Pacific mainline route across the Canadian Rockies which westbound travelers are treated to from Calgary to Kamloops in daylight. The only better route is the old Kettle Valley Line of the Canadian Pacific.
3. Olympian Hiawatha. The route across Wisconsin is unimposing but very scenic in it's own right. It parallels the river for over 100 miles into St. Paul which is nice. The Rocky Mountain crossing is spectacular with several viaducts and tunnels. Including one that the train leaves the tunnel straight onto a large viaduct. The route across the Cascades was also spectacular over Snoqualmie Pass. If you are wondering why this isn't my No. 2 it's mostly because the Mountaineer is impossible not to put in the tied for first column.
4. The City of Portland. Three words describe this route. Columbia River Gorge!!!! The route across the midwest to at least Cheyanne is fairly dull and not really exciting. But once you start getting into the northwest it gradually gets better. But once you get into the Gorge it's AMAZING.
5. Empire Builder. The highlight of the route it shares with the North Coast Limited over the Burlington Route. The train's schedule doesn't provide much daylight running in the Rockies and the Cascades. Which is why it landed the worst spot. The Western Star was far better.
Equipment
1. North Coast Limited. Hands down this train had amazing equipment. 4 dome cars per train, two of which were the rare dome/sleepers that we're only built for the Northern Pacific. Then you have the lovely Lewis & Clark Travelers Rest lounge cars. Towards the end of it's run it also had SlumberCoaches which ruined the two tone green paint, but provided a budget sleeper.
2. The City of Portland. Union Pacific equipment has always been consistently above average for starters. Secondly the dome diners just can't be beat.
3. The Olympian Hiawatha. What can I say Super Domes and Skytop lounges. But you only had one dome car per train the least of all of the contenders with dome cars. The Skytop was unique however.
4. The Empire Builder. Another train with four domes per train, including a full dome. But other then that I don't think it was particularly note worthy however the paint was sharp.
5. The Mountaineer. It was a heavyweight train so the ride was probably much smoother in the heavier cars. It did have a one of a kind piece of equipment a open air observation where most of the car body was covered but had no glass in the wide windows. Allowing people to get fresh air.
Food
Something that I can actually talk about seeing I've made a lot of these dishes.
1. North Coast Limited. Can't touch that Big Baked Potato with anything else.
And a four way tie for second because the rest weren't remarkable.
Schedule
1. City of Portland. By far the fastest option into and out of the Pacific Northwest. With a very fast 40.5 hour trip.
2. North Coast Limited it may have been two hours longer than the Empire Builder but it's route was timed better for the scenery, which is what earned it this rank.
3. The Empire Builder just because it's a quick 43 hour trip.
4. Olympian Hiawatha it's still fairly fast at 45 hr 45 minutes but it includes a lot of the scenic portions in daylight in both directions.
5. The Mountaineer. By far the slowest trip of them all with a 59 hour carding. Which is not a great carding, made only worse by the fact it does not originate in Chicago.
Overall the train that I have deemed the best is the North Coast Limited. I would really love to see all of the former NP cars get together for a charter on the Montana Rail Link ex Northern Pacific main line. There is almost enough equipment remaining to run a complete consist minus locomotives.