The Sierra Nevada range was by far the more difficult for several reasons. The Rockies rise and fall more gradually and it was easy to develop trails there that did not overly challenge the oxen, people or wagons. In addition, since the trip was usually undertaken as a spring-to-autumn endeavor, the ascent/descent of the Rockies was usually undertaken in relatively good weather.
The Sierra, on the other hand, is a newer range and so its escarpments are more dramatic. It is more difficult to find a passable trail across the mountains, and the trails that were developed were steeper (particularly on the ascent from the east). In addition, people, livestock, and equipment tackled this obstacle after the grueling majority of the journey - including crossing the Forty-Mile Desert. And finally, travelers typically reached the eastern foot of the Sierra just as the first storms were closing in. This year, for example, there were chains and snow-tire controls crossing Donner Summit at least once in September, so it was easy to be surprised by an early storm - as happened with the infamous Donner Party.