When Lewis & Clark made thier trek, they were crossing a contigous "wilderness", at least from the Euro-American standpoint. However they traveled on the easiest routes given the level transportation technology at the time. Travelers over the next several decades used similar routes and hence 'settled' along these routes.
Today the wilderness areas tend to be remote and rugged, since they were by and large the most inconvient places to travel and 'settle' and hence have been bypassed during the 160+ years between L&C and the begining of federal protection of these wildernesses (The Wilderness Act).
Which brings me to my point. If a traveler today wanted to experience landscape approximating what L&C saw, the route of travel should not include the actual L&C route. Most of the river-ways have been damned. Any dam below a point on a river restricts or prevents migrating fish from returning to thier spawning grounds. Any dam above a point on a river prevents the natural cycle of high and low water flow.
Much of the overland travel paths through valleys have been paved. Only crossing some of the mountain passes (Lemhi, Lost & Lolo) can one follow thier route without experiencing major influences of the modern world. Even in these areas, the density of the trees is much much higher than 200 yrs ago, while the size of them is much smaller.
I experienced some of this area first hand in 2002 with a road trip across Lolo pass, and eventially along the Columbia River. The area of Lolo pass that I tried to hike was overgrown with small trees and brush, whereas L&C encountered the trunks of very large trees.
We could have interesting discussions about why the forests are so different now than then. I suppose that clear-cut logging and fire suppression are the biggest influences.