Let's face it. Custom is always better. If you are running an ecommerce site, nothing beats custom system that is done just for your needs. If you'are selling books, you might have your own set of specific features, if you'are selling cars, it may be a completely different set.
Having custom ecommerce system is like having a magic wand, all the features are possible and available to you. But magic comes with a price.
Only big companies with hefty budgets and huge number of programmers can afford systems designed specifically for their own use.
For smaller guys that sell gift packages, candy or diaper cakes for example it makes sense to use what is available.
And in most cases it is very cost effective to use a hosted solution. An ecommerce solution developed with wide variety of merchants in sight, that is hosted administered and supported by experienced third party.
It is cost effective but it is limited too. Here comes the challenge of finding a solutions that suits specific needs of your business.
You have to get good understanding of available options to make the right choice.