Defining elements of a research project as assets or entries?
Actually, there's a brilliant plugin called Embedded Assets, which lets you manage YouTube links and other embeddable media like first rate citizen Assets in Craft. I highly recommend it.

As for the more general question of whether to go with Entries or Assets – it's difficult to give a solid recommendation without knowing more about your project and its requirements, and it'll also probably come down to choice and preference a little bit. 

I'm also not totally sure where you're going in regards to relatedTo, but again – Assets are first rate citizens in Craft, and they aren't limited in their capabilities compared to other types of content like Entries or Categories – certainly not when it comes to relations. Assets can be related to Entries, Categories, other Assets – sky's the limit.

Anyway – based on what you're describing, I would probably go for an Assets-only solution, rather than having Entries wrapping Assets. When the actual content is a file, and everything else is basically metadata, this is probably far the more elegant and effective solution.

Depending on your requirements, the only thing you may have to work around is the fact that Assets have no URLs (beyond the actual file URL, of course), nor can Asset sources be assigned a default entry template like e.g. Entries or Categories. For listing templates, search results etc. you can always rely on Craft routing your template filenames as URIs and then just create a craft.assets template query to fetch the Assets you need, but if you need to link to an individual Asset, you'll probably need to create a custom route.