Peru (and Bolivia) in 13 days

Its not really worth going all the way to la paz to only spend 1 day there and then backtrack. La Paz is nice but its not one of the highlights of Bolivia, and you would probably get a lot more out of spending that time in Peru.

Its also not really worth going into Bolivia to just spend a day at copacabana. Copacabana is nice enough, but mainly just a jumping off point for isla del Sol, which is beautiful.

With 13 days there is more than enough to keep you busy in south Peru.

With only 13 days I would definitely focus on Peru as well. Cruz del Sur buses are good but there are many other bus companies (we used Oltursa, PeruBus, Civa...). If you have 13 full days you could: go to Huacachina on day 1. It might be worth it to take a cheap hotel room even if you are not staying the night so you can take a shower after the dune buggy ride and sandboarding. Arequipa is nice for a day but the highlight for us was hiking in the Colca Canyon. You need at least two days if you want to do that. We had 30 days and didn't make it to Lake Titicaca. I hear though that an overnight on one of the islands would be great. So then you would have 4 days left for Cusco, the Sacred Valley and MP. Lots to see and do there. The Sacred Valley has Pisac, Chinchero, Moray, the Maras salineras and Ollantaytambo. Then there is Cusco and the ruins north and south of Cusco. Lots of hiking possibilities as well. We stayed in that area for 9 days. For Machu Picchu you have to decide how you want to get there. I assume by train as you don't have much time. You can take a train from Ollantaytambo to Aguas Calientes. Then a bus up to Machu Picchu. If you want to climb one of the mountains in MP you should decide which one. Huayna Picchu is very popular and you need to buy tickets in advance. If you just want to visit MP or visit MP and climb MP Montana (that is what we did) you can wait a bit longer to buy tickets. You can check availability and buy tickets here:

http://www.machupicchu.gob.pe/

You should also buy your train tickets online (Peru Rail or Inca Rail).

When you are done in Cusco fly back to Lima and spend a day there.

cut out the 2 days in Lima , not really a lot to see there . get the Lima - Cusco flight as it is one of the few affordable flights in South America

There's a lot to see in Lima, if you like history and architecture.

I agree; if you only have 13 days, don't go to Bolivia at all. It's not worthwhile going all the way to La Paz. You can visit islands out on Lake Titicaca from Puno; there's no special need to go to Copacabana. You should use more time for Cusco, and for Arequipa, and do an overnight trip down into the Colca canyon.

Thank you all so much for your replies! I'll be following all of your useful advice!

Hola.
We have been to Peru 3 times and once to Bolivia (you can see our blog in spanish... with infos)... Long routes and tiring... altitude... you´ll get sick!
13 days, almost IMPOSSIBLE so many things. Even for your southern Peru route it´s quite limited. You need at least 5 days for Cusco and Machu Pichu... many small villages too.
Cruz del Sur: they do good online promotions if not expensive. Same for Oltursa.
If not directly at the terminals many other good companies and much much cheaper.
Enjoy! Take it easy. Less can be more! True for South America.

It sounds like you did a similar trip to what my friend and I are about to do in November for 23 days. Flying into Lima and doing south Peru. We'll be doing lots of hiking, alongside the cultural stuff too. Is there any packing tips you have? I'm debating whether I should bring my sleeping bag or just rent one. I'll be bringing the typical layers for warmth, as well as my puffy jacket, hiking pants/shorts, etc. Any insight would be greatly appreciated. I've been watching the weather and it looks like the weather could be pretty rainy...

We had 30 days and spent a day in Lima and 11 days in northern Peru. Then we went to Cusco, Sacred Valley, Machu Picchu, Arequipa and the Colca Canyon, Huacachina and Paracas. We hiked quite a lot in the Sacred Valley. We did a day hike to Machu Picchu. We hiked up MP Montana. And we hiked in the Colca Canyon for 3 days. That was in January. We were expecting rain but it hardly rained (the rain came later this year because of El Nino). As for packing. Pack light! I had quick-dry hiking pants, hiking boots, a fleece and a windbreaker rain jacket. We did not take sleeping bags. We did day hikes and in the Colca Canyon we slept in hostels.

Oh great...thank you for you input :)