I traveled alone, except for a two week section in Northern Argentina when I cycled with a friend I met. I really enjoyed doing the trip alone, I think I met more people that way.
The hardest part? Probably Bolivia overall. You will be cycling at high altitudes consistently for the first time, and it's hard to breath for a while. The roads are dirt, and they are roller coasters. It's completely exhausting, but also incredible. Also the it is the poorest country in South America, so outside of cities there are not alot of accommodations. It's all wild camping, or staying in really shabby inns in villages. Also people are less friendly than in the other countries I visited. It's a fairly noticeable difference, and one that many other cyclists I spoke with noticed too. I'm not sure why.
From Ushuaia to El Chalten, through Tierra Del Fuego and southern Patagonia was also really tough, due to the wind. It's the most insane wind I have ever experienced, most times it was impossible to ride more than 6-7 kph. It was hard to eat anything, because it was just shoot out of my hands. It was pretty miserable. But you are not doing that part, so don't worry about it!