I grew up in the area and remember what Emeryville was like before the train station. This was before the Powell Street Plaza and Bay Street shopping areas were built, and before they built the EmeryBay Public Market (which is really sad looking these days except for maybe Peet's Coffee). Back then the big landmark in town was the Judson Steel plant. I remember seeing sparks and molten steel flowing from the open door.
The Hilton Garden Inn is the oldest big hotel in town. It was a Holiday Inn for over 30 years and from the outside looks rather old. I stayed there once after a wedding party and inside it's extremely clean and well maintained. However, I'd recommend not making our mistake in reserving a "mountain view room". A better description would be "freeway" view, along with the noise level that comes with the territory. Although it's well maintained, they can't do much to reduce the noise short of gutting the entire building and installing sound insulation. There's traffic on I-80 24 hours, and you might have issues sleeping with all that noise.
The next oldest large hotel is the Four Points, which is nice but does look a bit older. The more modern looking Courtyard by Marriott is across from the Bay Street shopping area and close to the Ikea. The current Hyatt House has had several names - more recently Hyatt Summerfield Suites, and originally Woodfin Suites. The only thing I've done there was have a company meeting in one of their meeting rooms.
I guess another option would be the Extended Stay American right on the Oakland/Emeryville border, although you'd probably need a car. The Berkeley Marina DoubleTree is pretty nice too, but you'd need a car unless you use their complimentary shuttle. They say they'll send anyone up to three miles, and I think the Amtrak station is within that range.
