Hi, I can't help but agree that Magento is one ecommerce solution with many bells and whistles and not to mention with eBay backing it up, I can see how it is an obvious choice however, there are a few fatal flaws that people tend to overlook because of its big name support.
One flaw that I need to highlight and that has been seen a couple of times in this discussion is that Magento can be slower to run if you don't have the right set up for it. This may affect page loading which in turn can affect conversion rates which for an online merchant is a flaw hard to overlook. I always suggest testing out a solution first before committing to a full package. Many solutions offer FREE trials. Although the initial sign-up is time consuming, it is worth it in the long run.
I think a more coveted functionality online merchants look for today in ecommerce solutions is SEO. I think SEO is key to bringing an online store visibility in the sea of ecommerce sites. Two ecommerce solutions I have found (continuing on my last post) are BigCommerce and AmeriCommerce which can be considered to have the strongest SEO functionality for best ecommerce software [zippycart.com]