Two BIG differences: Content Area supports PERSONALIZATION (via visitor groups) and DISPLAY OPTIONS while IList<ContentReference> doesn't support either. Most authors like the flexibility that Content Area offers when it comes to dynamic content. 

Other than that Content Area client side model is more complex whereas IList<ContentReference> is more like an array of references ids. Content Area doesn’t implement the IEnumerable interface but needs to use FitlteredItems to get all the items. Content area also allows to create new blocks from the property itself. 

Great, 

thank you Aniket.

So, what would be then to reason to use IList? if ContentArea offers much functionality in the package?

I'd say semantics. Perhaps performance as well, you could cache the IList<ContentReference> harder, seeing as it lacks personalization. But generally, if for example this list of ContentReferene for some reason won't be directly rendered, but rather just passed to the client or used as data in the controller for the content, then you know you don't want any of the additional features ContentArea provides. So it offering more functionality is actually just more confusing for the editors, because you'd be ignoring it.