hello,
I also say option 1, but with a few additions, if you have the time. Firstly, Lima, in and out of that place quick (my opinion) then you say cusco, but there are 2 ways to cusco, lima direct route can be nasty, especially if its been raining a lot, stuck busses etc... and still a 16 - 24hr hour ride. Take the bus to arequipa (16hours) spend a few days there, really nice city, some awesome hikes if your into it, a few 18,000 plus foot mountains/volcanoe hikes (for beginners too!) or the colca canyon. From there go to puno , now puno (my opinon) not worth staying, dumpy town. UNLESS your doing the lake titicaca lake tour. If so, try and do the overnight one to spend the night with a local family on one of the islands. then cusco, or skip puno, and do arequipa to cusco one shot. Then yes you will have to backtrack, and go back through puno on the way to la paz, so you could make your puno stop at this point? After la paz its a long bumpy ride south. If your like us, you'll love bolivia and want to see and experience more of it !! so maybe take the overnight to uyunni. Do the 3 day salt flat tour, while the tour and hostels and food are pretty rough. MAn the scenery is awesome, salt flats are cool, but the next few days in the high mountains are sooo awesome, really makes you feel like you been in the back country of bolivia, if only for 3 days. The take the train to villazon (MUCH better option than crap dirt road bus) once there you have to walk across border, then take bus to salta (6 hours) Salta is nice, worth a few days. its about 27 hour bus ride to buenos aires from salta, or a $125 u.s. plane ticket.... AFter BA, then off to mendoza (note... if your into wine and tasting's, and wineries, you'll love it here, if your not into wine, its still very nice, but only worth a few days) From mendoza over the andes to santiago (short 5 hour bus ride)
The atamaca desert, well its a desert, we hit calama to go to the copper mines, but honestly from the border of chile all the way south to santiago is one big long boring desert !!! San pedro de atamaca is a cool town, but if your going to uyunni i think you get the better of those 2 options, in mountains scenery, salt flats, etc...Theres still soo many variables, and youll see once there how many times you say, we should of, or could of, or etc.. haha. its a crap shoot.
(just my opinon)
thanks