@brianlewis, In your first paragraph, it sounds like you are comparing a negative from a 135 camera to a crop from a 120 negative, so two different lenses. If I understand correctly, your second paragraph compares two different negatives from the same camera and lens.
If using the same film type for all shots, I would guess the grain would be the same, as would the
potential sharpness as determined by the film. The
actual sharpness however, could be different in the first scenario due to comparing two different lenses 135 vs. 120).
Generally speaking, I believe it is slightly harder to make the larger lenses which go with larger format film to the same degree of precision as lenses made for the 135 format. I am sure there are exceptions, but I think the resolving power may be slightly better for some 35mm camera lenses than for some medium format lenses? If true, then you might get a slightly sharper image from the 35mm camera than from a 24mm x 36mm crop of a medium format negative, at least in the center of the frame. Considering the crop from medium format film avoids the corners, corner sharpness might suffer less? Just guessing.
Edited to add: Whether your scanning process can capture the slight difference in resolving power is a different discussion. That is, if your scanning process is the limiting factor in final sharpness, it won't make any difference which way you do it.