1

There is no way to bypass La Paz if you want to get to Copa. You original plan sounds good, either take a train or fly to Uyuni and on way back go trough Potosi and Sucre that are both very interesting.
This is much better option than expensive and touristy San Pedro.

2

If you have the time and are not on a tight budget you could combine your 2 options, ie go to Uyuni via Sucre and Potosi, on to San Pedro and back to La Paz via N Chile. Chile is considerably more expensive than Bolivia, and San Pedro is more expensive than the rest of northern Chile.

If you plan to stay in Bolivia you can't go to Copa without passing La Paz. You could do an even bigger loop and carry on from Arica into Peru and get to Copa via Arequipa and Puno if you had time.

3

Thanks
Is the atacama desert and san Pedro interesting enough to warrant this big loop or better to focus the time around Bolivia?

4

#3 It's not in my opinion

5

Depends what your interests are and how much time you have. The scenery on the Uyuni tours is more impressive than what San Pedro has to offer imo. If you like historic colonial towns, indigenous people and culture and generally being in a country that is very different to Europe / US you'll be better off in Bolivia. If you fancy going down to the coast, beaches (with cold water) for a few days do the Chile loop. The Atacama desert area has enough of interest for few days (Iquique would be the most interesting town). Another factor might be the weather, November is getting close to rainy season in Bolivia and it can be quite variable, should be mostly hot and sunny down on the coast.

6

It's worth adding another factor: budget. Chile is much more expensive and I would rather spend this money in it's southern part that is much more impressive an unique.
Chilean beaches are mediocre at best, for beaches Colombia and Brazil are the place to go.