We get a combo of both,
JR is great for lots of day trips from a home base, but doesn't work out ahead if going from 1 side of the country to another.
Going from Tokyo to Sapporo on JR takes +10 hours instead of 1.5hr plane. To extend the JR pass another week costs around $180AUD/pp at the moment. Local train rides without the coverage on Suica only cost around $1/trip. We'll be activating our JR Passes in Hiroshima, and then bouncing around to Kyoto, Osaka, and back to Tokyo, perfect for those distance with speed, time etc.
Long distance, the link in this post works out well ahead of JR, in time and likely cost..