I have a couple of ecommerce SEO client, they have the same setup, hundreds of pages with duplicate content on other similar ecommerce sites. However we were able to ranked them on the Top of Google UK for long tail product keywords. What we did are the following
1. Pick the main keywords and associate them with their respective pages during link building.
2. Performed onsite SEO by modifying the (title, meta tags, html tags and contents) of those pages suited to the main keywords and similar/synonyms.
3. Perform balance link building on these keywords and their respective pages
Their rankings have started to climb gradually within 1-2 months, and now some of their main keywords are on Top 1 & mid page 1.