The problem is that you pretty much can't pick another.
The trajectory chosen was to reduce mission time.
If you have 9 years, then pretty much the only way you can do a pluto probe is blasting past at >10km/s.
If you try to make the trajectory more gentle, then yes, you can do this - a hohmann transfer - but this will take literally a hundred years. There is nothing close to pluto that can slow you down meaningfully at all with a gravitational assist.
Nuclear powered ion engines, nuclear rockets (dusty fission rocket), and aerobraking are all in principle possible, but they all have their own risks.