As far as I understand, the next generation of heavy lift vehicles (i.e. Starship, New Glenn, SLS) will not allow us to do better than a Hohmann transfer. And that would still mean waiting for the launch window to Jupiter (period 1.1 years) and a transfer of 3.7 years. So Clipper's cruise of 5.5 years really isn't so bad.
Future space probes will likely continue to save delta-v by taking a slightly slower trajectory with gravity assists.
Starship could open up a lot of options. There’s no reason it couldn’t launch a small probe loaded to the gills with fuel and engines and make a shorter trip.
Hohmann transfers (the most efficient path) take a fixed amount of delta-V, so how much fuel you have does not really matter. You could probably find a quicker path if you are willing to sacrifice some efficiency, but even then it is going to take several years to get there with current technology. Since probes don't really care about travel time, might as well take the most efficient path so that you have fuel left over for interesting maneuvers near the destination.
Future space probes will likely continue to save delta-v by taking a slightly slower trajectory with gravity assists.