Migrating Data from SQL Server 2005 to 2016
Max gave a decent answer which I will upvote once I'm done typing this alternate view up.

I am not a fan of restoring system databases when doing an upgrade migration and I prefer doing migrations over in place upgrades as I discussed in this lengthy answer to another question.

Basically I like to start "fresh" when I do a migration. I find that playing with system database migrations and upgrades through restore to sometimes cause frustrations with the restores and it can carry over potential sins. 

You also asked about indexes, stored procedures, views. Those items at the database level should all live inside of a user database. So when you restore database X to the new server, all of the database objects (Tables, Users, Views, Procs, Functions, etc) will be there as well. 

What exist in the system databases are jobs, logins, alerts, linked servers, encryption keys, etc. Instance level items.

I like to review those and migrate over what I need using various scripts - lately that is the DBATools.Io powershell scripts. I like using their script to copy sql logins especially, because it handles the SQL authenticated users keeping their passwords and security identifiers the same so the database users from those logins will work. They also have an entire SQL Server migration command which runs their sub commands to copy over the items I typically would copy over. 

I do not believe Max to be wrong with that answer  hence the upvote. I just have had more success and more luck and feel more comfortable migrating to new instead of trying to restore over system databases between versions. I would say that I've honestly can't remember the last time I did a version upgrade migration and didn't do it this way instead of restoring the system databases.