Bob-
You probably already know this but Panda is about content quality and penguin is about link profile quality. Here is what we have done recently for some of our ecommerce clients that have come to us because they had panda or penguin update issues.
1.) Definitely need to look at your product descriptions to make them unique. We had a large client with 4 ecommerce stores and a large number of similar products that got hammered by Panda. We ended up rewriting 80% of their content related to similar products and got them back on track to almost the same exact position before the panda update. If you are in a situation where you need to prove the concept or it seems insurmountable, then just focus on rewriting descriptions for your top 100-150 products to do a mini test with the content strategy. You will see positive results or will avoid the penalty.
2.) We have worked with several ecommerce companies that have told us they dont have a large amount of "inter-linking" going on but when we did some analysis we found thousands of links between the sites they owned. Their issue was related to the fact they had several seo people that kept adding additional links between the sites without really knowing what the guy before them had done. Just make sure your interlinking doesnt look forced and it makes sense. To link a category page to a product page to a video page can make sense. To have 100 links between 2 pages on 2 different sites looks forced. Not good.
Obviously if you are creating a new site and it isnt linked to your other site, you will be avoiding any issues related to the penguin update. But if there are vaible opportunities to link between sites that isnt overdone, then dont lose that opportunity altogether.
Hope this helps. Good luck.
Mark