Blessed with an incredibly efficient transit system, not only do trains run like clockwork, they are also insanely clean and safe.
You have to get out of your head the idea of singular subway system as you would have in New York City or the S-Bahn and U-Bahn in Berlin.
Think of Tokyo Metro as the precision form of transit that can take you to the very specific corners of the city while the JR line is meant to take you to the major destinations of the city.
If you're just focusing on the best way to get around Tokyo, it's unlikely you'll need to take these but if you're thinking about a day trip up to Tochigi or Kichijoji for street food you'll be looking at one of these.
What ultimately makes Tokyo transportation so complex is that you can't just pay for a ticket on say Tokyo Metro and be able to switch to the JR line after with that same ticket.
For most visitors, picking up a Suica card at a JR station or a PASMO card at non-JR stations will make the most sense to nullify the complexities I mentioned above.