Personally, of the Union Square and the Embarcadero Center Plaza, I prefer the Embarcadero Center Plaza because it is bigger and, especially at night, the scenery is better because of the lights that will be lit for the Embarcadero buildings, the Bay Lights of the Bay Bridge and the Ferry Building in the background. Check out the video below.
What I like about the Union Square ice skating rink is the Christmas tree that provides a more holiday atmosphere.
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This is the Embarcadero Center Plaza ice skating rink:
This is a video showing the scenes around the Embarcadero Plaza lights:
This is the Union Square ice skating rink:
I will post a video of the Civic Center ice skating rink when it opens.