In the north, they keep discovering new archeological sites in the Trujillo-Chiclayo area. These are artifacts from groups that pre-date the Incas, such as the Moche and Chimu. The huge walled city of Chan Chan and the pyramids of the Sun and Moon near Trujillo as well as the pyramids and burial sites near Chiclayo and the nearby museums that display the valuable artifacts found, are just some of the places that are well worth visiting in this area that deserves to get more tourists. 2-3 days is probably the normal amount of time spent in this area. I think this is an under-appreciated area - particularly the pyramids
People used to spend as little time as possible in Lima, but now it has because a place to spend more time in. With the museums, the culinary scene, the nearby ruins (such as Pachacamac and Huaca Pucllana) and the Palomino Islands, you can spend 2-3 worthwhile days in Lima.
And don't forget the Amazon. Though the largest part of the Amazon basin is in Brazil, there are many lodges and cruises in Peru that offer abundant wildlife and local people to see. In general, I think you can see more wildlife from easily accessible lodges in Peru than you can from easily accessible lodges in Brazil because many of the Brazilian lodges are located near Manaus - a city of 2 million people.
Of course there are other areas, such as Arequipa/Colca Canyon, Huaraz, the far northern coast,etc. The recent earthquake in the Colca area has not affected tourism much at the present time (a couple of hotels were temporarily closed)
If you want to do group day tours to save money, then you will have to stick to the high traffic areas or go on a fixed departure group tour. If you do a private tour, then you can go to many other places and even go to the high traffic areas in a way that will allow you to avoid the crowds - such as doing the day's itinerary in reverse or starting at a different time.