More payment gateways for processing orders. For example, we always use http://www.protx.com for payments to the bank account. Google and Paypal fine, but on their own, they make a site look cheap.
The SEO urls
From what I understand, you have to manually add in the string conversion. This would be better if it was automatic for all categories,pages and products. i.e. /shop/category/3/big-red-shoes_1.html | /shop/pages/2/this-is-the-page-title.html example: http://www.maybebabylingerie.com
Auto image resize
This has been brought up before, but it’s important. People updating their site, don’t want to go through the process of scaling all imagesx2 for upload
The whole structure of trying to integrate a custom look and feel is a bit confusing with seperate folders for the html and the css/images. It would be better if they were oganised into the one theme folder with html/css/images. Also the phtml files. I know this is common, but they don’t play well with editors/wysiwyg. Why not just .php?