The reason why the New Horizons spacecraft did a very quick flyby of Pluto is pretty simple.
Relative velocity.
The spacecraft was launched in 2006, on a trajectory to Jupiter, where it made use of that planet's gravity to depart at an even faster velocity (relative to the sun and planets.) Go screaming outbound as fast as possible, so it would be possible to reach Pluto in a reasonable length of time (by the standards of human careers.)
New Horizons reached Pluto in 2015 – moving at a speed of 30,000 miles per hour!
At that speed, it would have been totally impractical for the spacecraft to slow down and linger in the vicinity of Pluto.
To an order of magnitude, stopping at Pluto would have taken about as much energy as it took to launch the spacecraft in the first place. And it's a tiny probe, not something that could lug along a huge rocket of the size needed to do that kind of maneuver.
The price of getting a spacecraft to Pluto as fast as that, was it had to be a quick flyby.
The Pioneer and Voyager spacecraft to the outer solar system did the same thing. Galileo and Cassini went into orbit around Jupiter and Saturn, but they were also moving more slowly, to make that possible.
As for the pass of Ultima Thule, that was an extra bonus. NASA carefully searched the area of sky where New Horizons would be flying after Pluto to try to discover anything small in the area that the probe could fly past, and eventually found one.
Here's a neat tidbit about Ultima Thule. The big surprise so far is that New Horizons is finding that the light level is steady. This is not expected; as anything (planet, moon, etc) spins and presents different sides, it will vary slightly in observed brightness. This is called a "light curve". But New Horizons isn't seeing any variation. Might mean the object's pole is pointed towards the sun and spacecraft, so we're flying in end-on. Might mean it's spinning extremely slowly. In any case, that's the big surprise so far.
https://behindtheblack.com/behind-the-black/points-of-information/no-rotational-light-curve-from-ultima-thule/
If you want to get crazy (ha), aliens knew we were looking for something to fly past in that direction, and parked a spaceship in the area New Horizons would have to traverse after zipping past Pluto, knowing we'd find it and take a peek. So it's not spinning because it's artificial and waiting for us. (I don't take this seriously, just having fun)
Oh, and please don't say the Moon doesn't spin. It does, once a month, relative to the stars (and any inbound spacecraft coming to our planetary system would see the Moon spinning and showing a light curve). But it spins at the same rate it circles us (tidal locking) so we're kind of doing a dance together.