Include everything. You want Google to spider everything.
Let's take an example:
Two pages which talk about Llama Grooming, one which focuses on Llama Fur Enhancement, and the other that focuses on Llama Fur Lustre.
The content for both pages really is the same, just the SEO is a little different for each.
Your main page: www.llamas.com/lfe.com (Llama Fur Enhancement) has all the copy SEO'd for Llama Fur Enhancement. Your "alternate" page has the same copy, but optimized for Llama Fur Lustre with a Canonical REL tag back to the original page. If you omit the second page from the Sitemap, it doesn't get spidered, then what's the point? Both need to be spidered, but the Canonical REL tag tells it which is the "official" page so you don't get dinged for duplicate content.
Capice?
Jim