A few years ago I took an interest in a distribution called Linspire. It was quite an ambitious undertaking that may have been before it's time. I think they gave up too early. But anyway, they had a website called cnr.com which stood for Click N Run. You could download and install all your apps directly from this website. You could also purchase commercial software from there. I believe you could link it directly to the repos too.
I love Linux Mint. It is the best execution of a distro I have used yet. I think it would be great to create an analogous website. Then you could bypass Software Manager. Mint could also sell some of the fine commercial applications for Linux there too. This would only boost the development of Mint Linux. Heck, Apple is making zillion at their Apple store and Microsoft is headed down the same road. Why not distribute much of this great FOSS using a similar means?
I vote for http://www.mintstore.com. I think the domain is for sale too. I hope they wouldn't want too much.