Here are my thoughts on the questions you've posed:
Which of the places on the list are notable enough for separate articles (if they don't have one now)?  I've added links to articles where I could them.  I'd say articles are also needed at least for Sugar Creek,  Red Butte, Rocky Ridge, Echo Canyon, and Emigration Canyon.  A couple of points of interest that could be added are Genoa, Nebraska (settled by the Latter-day Saints as a supply point) and This Is The Place Heritage Park.  I'm sure other landmarks will be identified with additional research.
Which places could be reasonably combined in sections, like the eastern Wyoming sites? Some suggested sections:  Iowa (mostly covering the 1840s); the Missouri River area (Winter Quarters / Kanesville / Florence); Missouri River to Fort Laramie; For Laramie to Fort Bridger (with a focus on the handcart companies); and Fort Bridger to Salt Lake Valley.  The Iowa section could include a brief subsection on the route used by the handcart companies from Iowa City to Florence.
And how are we to deal with elapsed time, as early companies had different experiences than later companies?  One chunk for geography and another for linear time? I think the organization of the Mormon Trail article should focus on geography.  Content that is intrinsically chronological could be moved to the Mormon Pioneer article.  Would it make sense to tackle both of these articles at once to try to ensure that they compliment each other without simply being repetitive?—