Hi David,
You're definitely on the right track with bringing all the sites together. Then you've got everything in the one place and will only have to focus on doing SEO, content and link building for the single site. Plus all your authority can be amalgamated together via 301 redirect (provided these are clean and don't have bad backlinks), which will help with rankings.
Aside from general keyword research targeting via meta data configuration, I'll recommend you implement a solid content strategy. If you're going to be putting out a lot of products and you're duplicating the content, I'd consider canonicalising it back to the original source and rewriting any products have big search volume. Secondly, I'd make sure you have at least 200 words of content on your category pages using LSI keywords to boost on-page relevance and get some quality links built to these pages. If you follow that strategy you should get some good results. I wrote a blog post about Google Hummingbird and optimising you content with LSI keywords, you can check it out here.
In terms of an actual ecommerce platform, I've worked with Magento a lot with big ecommerce sites. Seems to have a lot of functionality with plug-ins, a lot of big brand sites use it and it's built by eBay so they must be doing something right.
Here's a guide that highlights common issues with Magento: https://paulnrogers.com/magento-technical-seo-issues-to-look-out-for/
The most common issue I've seen is duplicate content that is caused by the /shopby/ directory. If you implement the below robots.txt file, you should see a lot of the unnecessary, dynamic URLs excluded.
I also recommend using siteliner.com to identify any internal duplicate content on the site.
##Magento SEO Improvements robots.txt
User-agent: *
Disallow: */index.php/
Disallow: */catalog/product_compare/
Disallow: */catalog/category/view/
Disallow: */catalog/product/view/
Disallow: */catalogsearch/
Disallow: */catalogue/product_compare/
Disallow: */catalogue/category/view/
Disallow: */catalogue/product/view/
Disallow: */cataloguesearch/
Disallow: */checkout/
Disallow: */control/
Disallow: */contacts/
Disallow: */customer/
Disallow: */customize/
Disallow: */newsletter/
Disallow: */poll/
Disallow: */review/
Disallow: */sendfriend/
Disallow: */shopby/
Disallow: */tag/
Disallow: */wishlist/
Disallow: */catalog/product/gallery/
Disallow: CVS
Disallow: .svn
Disallow: .idea
Disallow: .sql
Disallow: .tgz
Disallow: /admin/
## Do not crawl common Magento technical folders
Disallow: /app/
Disallow: /downloader/
Disallow: /errors/
Disallow: /includes/
Disallow: /lib/
Disallow: /pkginfo/
Disallow: /shell/
Disallow: /var/
## Do not crawl common Magento files
Disallow: /api.php
Disallow: /cron.php
Disallow: /cron.sh
Disallow: /error_log
Disallow: /get.php
Disallow: /install.php
Disallow: /LICENSE.html
Disallow: /LICENSE.txt
Disallow: /LICENSE_AFL.txt
Disallow: /README.txt
Disallow: /RELEASE_NOTES.txt
## Do not crawl sub category pages that are sorted or filtered.
Disallow: /*?dir*
Disallow: /*?dir=desc
Disallow: /*?dir=asc
Disallow: /*?limit=all
Disallow: /*?mode*
## Do not crawl 2-nd home page copy (example.com/index.php/). Uncomment it only if you activated Magento SEO URL
.
## Disallow: /index.php/
## Do not crawl links with session IDs
Disallow: /*?SID=
## Do not crawl checkout and user account pages
Disallow: /checkout/
Disallow: /onestepcheckout/
Disallow: /customer/
Disallow: /customer/account/
Disallow: /customer/account/login/
## Do not crawl seach pages and not-SEO optimized catalog links
Disallow: /catalogsearch/
Disallow: /catalog/product_compare/
Disallow: /catalog/category/view/
Disallow: /catalog/product/view/
## SERVER SETTINGS
## Do not crawl common server technical folders and files
Disallow: /cgi-bin/
Disallow: /cleanup.php
Disallow: /apc.php
Disallow: /memcache.php
Disallow: /phpinfo.php