What you need to remember, Google is very picky, and even if you submit all the subpages of your site, Google will index only part of it anyway.
More importantly, make sure that the cross-link of all pages is βeach other,β so make sure you make good use of the main navigation, breadcrumbs, footer links, etc. Because this is the main way googlebot will crawl your page.
Personally, I had a situation where after updating sitemap.xml Google immediately said that the new link in my sitemap was already indexed (because googlebot indexed it on its own before it was placed in the sitemap.xml file).
Conclusion - Add as many links as you can, and don't worry about the missing. Just make sure you update sitemap.xml once in a while (or do it programmatically).
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