I liked how this was handled in Spiderman 2018 - after major plot points, the main character would say 'looks like it'll take a while before the lab results (or whatever) come back, now's probably a good time to patrol the city', and the main quest wouldn't progress until you'd done at least one side activity - so if you wanted to just plow through the main quest it was just a small diversion, but it was also a great indicator that now was a nice time to spend some time playing around in the open world if you wanted to.