Only if….
1) you don’t like to sleep for hours next to The Mystery Passenger, who may have bathed a couple of days ago…maybe…and gawd knows what he’ll want to talk to you about when he wakes up and stops snoring,
2) you don’t mind the free breakfast in the morning in the diner car, or
3) you’re a big fan of sleeping in a flat bed at night (though I have to warn you, the bed might be a touch on the short side).
Go for it. For Amtrak, that’s cheap! And you never know if it’ll be your last chance to ride a crosscountry train in the US.

Pedantry and geekery
Actually, Metra is “commuter rail”, which is usually lumped with “heavy rail”, see the discussion at light rail.
Metra is cool in that it uses gallery or bilevel cars. Although an article in Wikipedia seems to suggest that the genre started in 1970 in Canada, the Illinois Railway Museum has C&NW gallery cars built in 1955.

Ah, now that’s one I can’t help you with. Methinks the Radiowuff from Chambana has more experience with Amtrak overnight trips than I and would be the better person to ask.
Incidentally, I did find another way for you to get out to the hotel if you’re interested:
Metra (light rail) Union Pacific District Northwest Line from the Madison Street Station to the Palatine Station, then you can pick up Pace (suburban bus system) Bus Route #699 southbound down to Woodfield Mall. Metra is without a doubt one of the best light rail systems I’ve been on, and if you’re a train geek and haven’t OD’ed on trains by the time you get to Chicago, it’s a very pleasant ride.

Ok, one more q
amtrak called me with the option to upgrade my trip up to chicago to a minisleeper for $50.
Is it worth it?

I think it is. The views are fantastic, but keep in mind, if the weather not good it’s a waste. The good news: after you go in, you take an elevator down to the the sub-basement, where you buy tickets, etc. They have a sign as you walk in saying what the visibility is at the top of the building; anything less than 20 miles visibility, I’d suggest turning around and walking out.
Note that the entrance to the Skydeck is not the same as the entrance to the rest of the building. The only entrance to the Skydeck is on the south side of the building, on Jackson. All bags are searched and X-rayed, and you have to go through a metal detector. For what it’s worth, I’d stow your bags at Union Station.
Union Station does indeed have baggage lockers available; expect to pay about $3.00 – $6.00 for a few hours’ storage. Looking at this handy map, it looks like they’re located near tracks 26, 28, and 30.
And I can’t blame you about public transit – I’m the same way. Fortunately, Chicago is a great city for public transit.