Of the hotels the OP mentioned, I have stayed at the W and I would not describe it as intimate. The lobby is buzzing and very crowded, particularly be people spilling over from the cafe and, during my stay, by buses of people unloading. Rooms are great but it doesn't sound quite right.
If between Embarcadero and Union Square is required, I would recommend the Hotel Vitale.
http://www.jdvhotels.com/hotels/sanfrancisco/vitale
The issue with that area of San Francisco is that most of the hotels are the large, dull chains. There are many more interesting boutique style hotels in the more residential areas, often in converted Victorian terraces and some of these might offer the style required, if not the location - but that's for the OP to decide.