Trekking independently – making all your own arrangements, carrying your own pack and staying in lodges – saves money and may give you more freedom or flexibility on the trail. In terms of route choice, however, it’s more limiting than an organized trek.
Doing it yourself gives you more control over many aspects of the trek: you can go at your own pace, stop when and where you like, choose your travelling companions and take rest days or side trips as you please. The downside is that you have to spend a day or three lining up bus or plane tickets, renting equipment, buying supplies and perhaps tracking down a porter or guide. A more serious drawback is that you’re effectively confined to the more popular trails; trekking to remote areas is difficult unless you speak Nepali or you’re prepared to deal with considerable porter logistics.
An independent trek is likely to be less comfortable than one arranged through an agency. Lodges can be noisy and lacking in privacy, and there may be long waits for food of dubious quality. The active social scene in lodges goes a long way to compensating for this, however – even if you start out alone, you’ll quickly meet up with potential companions.
By not being part of a group, you’re better placed to learn from Nepali ways rather than forcing local people to adapt to yours. Equally important, a high proportion of the money you spend goes directly to the local economy (whereas most of the money paid to trekking agencies goes no further than Kathmandu, and often finds its way overseas). However, as an independent trekker you must guard against contributing to deforestation. If you or your porters or guides order meals cooked over wood fires, you encourage innkeepers to cut down more trees. Fortunately, kerosene is replacing wood in the most popular areas.