Field Collection vs Entity Reference
This is a question I make myself when facing new projects, Field Collection vs Entity Reference + custom entity or if the structure is simple, Field Collection vs custom field with several db columns / Multifield. Here's my opinion based in my experience.

Multifield is a great concept, it'd be a "lightweight" version of field collection, instead of creating an entity structure with relationships, it covers the simple use cases without creating the entity. It has a number of issues, though, such as not complete Features integration, not really multilingual etc (so if you plan to use this, contributions will be probably really welcome).

Field Collection is a great solution if you're doing a site that can be done just with a few tweaks here and there, it gives site builders a powerful tool to create complex structures without worrying much about the internals. It will basically create an entity that relates with the "host" entity by the ids, allowing to add fields to it and everything.
The disadvantages would come in the knowledge of the internals of Field collection that you need to perform complex operations such as managing a Field Collection with an Entity Reference on it, or migrate data. As it is a generic tool, it'd be fairly complicated to go one step beyond.

Another option you've got there is using ECK with Entity Reference, but my experience with this has been a disaster so far, I find it way easier to create the entity type by code without the helper.

It's a matter of what you need and what's the best fit for your project, if you've got the time and the developers to create entity types that relate with your data model through Entity Reference, you'll have more control over what's happening with your data structures, but then you're the "responsible" for that too.

After testing a while with all the solutions describe above, in my team we always go for the entity types + ER, but I can see that for small projects, without data migration or a complicated i18n setup, Field Collection is just the fastest way to go.