Behold, my unsolicited comprehensive comparison of the HR Embarcadero vs the GH Union square, after staying at both back-to-back these past two weeks:
Seems like they are down to only a few floors remaining with the renovation at the HR -- supposedly all rooms are either renovated or under construction right now. So no rooms are being given to guests anymore with the old furniture.
For what it's worth -- I didn't notice the construction at all except for a bit longer wait times at the elevator.
Gotta say: With the renovated rooms, I think this is a better offering than the GH as both hotels stand right now. And I used to be a GH fan.
Yes, the GH has the club open again, but it's starting to get crowded and I found the food offerings to be lackluster. You can potentially make a dinner out of the evening appetizers, but you'd have to like the single hot item of the day, otherwise you are left with an iceberg lettuce salad and chips. On the first night I was there, they were serving some kind of make-your-own ground meat tortilla with white sauce. It was good -- but neither attendant knew what kind of meat it was nor what the white sauce was (greek yogurt something?). Don't know what to make of that. After watching a kid stick his finger in the white sauce I opted to walk to Chipotle instead of getting seconds

.
I'd much rather take the $15 daily credit at the market in the HR. Plus, the HR breakfast goes until 11:00AM every day which is an hour longer than the GH on weekdays. Both have a Starbucks across the street from their lobbies -- which I sometimes opt for as well.
HR with the renovation has nicer rooms, period. More spacious than the GH rooms, although some are a bit under-furnished (ex. could've fit a couch but only put a chair). Some GH bathrooms are more spacious, but the tubs and layout are very dated. Plus, out of my 6 past stays at the GH, 4 of the rooms had toilet issues that caused the flushing to be ridiculously loud with a kind of metal-grinding noise. It will wake everyone in the room. No idea what is causing it but it's a widespread issue. Some GH rooms have a bit nicer views, but I've found bay-facing rooms to be a tough upgrade for Globalists. You will get a high floor, it'll just be facing south or west likely. In that case, the "room in the sky" feeling is still nice, but I personally prefer the balcony rooms at the HR that face the bay and are a reliable upgrade for Globs.
Speaking of which, HR's balcony rooms are really underrated. Even though the GH club has exceptional views of the bay and downtown, I'd rather sit on the balcony with an evening drink. Point to the GH, though: self-serve alcohol in the club is $4 or $5 a glass. HR it's $12+ at the bar otherwise you have to go shopping

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GH has problems with elevator noise in about a third of their rooms (I always tell people to request corner rooms), while HR rooms are reliably quiet -- especially on high floors. Pro tip: At the GH, you will know if you were assigned a problem room within 5 minutes of check-in and should request a room change at that point. Don't expect it to get better during the night. They put those earplugs on the nightstand for a reason...
GH restaurant is still closed for dinner -- and the bar is ok for drinks, but you can do better just by walking a bit or taking a quick Uber (I am in my mid-20s so take this with a grain of salt

). GH Bar food is lackluster, but fine if you are tired from a day of travel or something. HR bar is comparable for food and drink but lower priced by about 20%.
HR is a better location for tourists during the summer. Probably a toss-up in the winter because Union Square tends to perk up a bit around then.
I do prefer the gym at the GH, perhaps just for the view, but the HR one is comparable. It's just visible via a glass partition to people in the lobby so that's a bit odd...
I think the GH has a chance to get back on top, but that'd require three things:
1) Re-opening the restaurant for lunch and dinner.
2) Renovating the rooms to take them out of the 90s and adding soundproofing to the ones with issues. Also, please fix the toilets.
3) Expanding the food offering in the Grand Club -- and maybe making it a bit larger?
For now, I'll tend towards booking the HR I think -- unless I have a reason to be close to Union Square.