Ubercart

Well, your method of approach all depends on the way you need to organise and theme the content. Since the product content type is built into Ubercart I think I would try and leave that alone (or expand it with CCK fields if needed - the point is not to copy it to another content type). Use taxonomy to categorise your products into merchants. You can make a vocabulary called Merchant and then make terms for each merchant so you can assign products to a specific merchant. To display the products you should use Views and add a filter for taxonomy terms. Alternatively you could use arguments in Views to control the merchant products by the URL but this can be a bit tricky. It's probably best to create multiple views (at least one for each merchant).

I'm far from an expert at this so I hope my advice isn't erroneous. Maybe someone else can chip-in with some more comments.

just brainstorming a little.

if the site was constructed with organic groups could that make it easier to define the theme for each merchant, without creating a new type for each?
This way each merchant could administer their own store while still being a part of the mall. are you looking to have the global store have its own theme?
take a look at taxonomy filter

Not to re-invent anything here but it sounds like ebay or googlebase privatized.
got any links to live betas yet?