It's not that small, and it's not a boutique, but I just spent two nights at the Adlon Kempinksi and was blown away.

The location is perfect. The building is beautiful. The staff are amazing.

The Arte Luise Kunst Hotel is a fun, funky place. The rooms aren't the ultimate lap of luxury but I think they more than qualify as "comfortable." And the hotel certainly has interesting design elements.

There was nothing we could find wrong with the Hotel De Rome in Berlin, which is a Rocco Forte hotel. The staff, the room, the service, etc. everything was first rate.
We'd highly recommend staying there.

I visit Berlin often for work and when in town I always make my stay at the Hotel Mandala. The interior design is wonderful, it is sleek but very warm and comfortable. The dining is superb and I am sure you'll enjoy the design of the guest suites. The baths are amazing as well and they are fully stocked with exotic toiletries including body honey, bath salt and bath tea, lotions, about a dozen soaps and a bamboo box of sea sponges. It is a wonderful place and the location is great!

Amid the energy of Berlin, The Ritz-Carlton welcomes guests with a gracious atmosphere and impeccable service. You may get the accommodation according to your preferences as many options are available.

The Ritz Carlton and Kempinski are the height of luxury but the smaller boutique style hotels have more of a Berlin feel. Depending on your budget http://en.escapio.com/boutique-hotels/berlin has a really good selection actually. What do you think?

You're absolutely right, Cocotravels. http://en.escapio.com/ looks like a really good website for those smaller hotels.