Bigger objects have greater gravity than smaller objects, therefore are more spheroid.
As we get better at observing, we'll see more objects that are less spheroid.
Similarly for Ultima Thule. They may have been able to find a different target, but it was very difficult to find any target at all in the first place (lots of Kuiper belt objects are known; the difficulty was finding one that could be reached by New Horizons). See this Twitter thread that was linked elsewhere: https://twitter.com/Alex_Parker/status/1077986070128668674
Pluto may be a KBO also. Further, it's possible some moons of the gas-giant planets are captured KBO's.
The unusual thing about Ultima Thule is that it's in a nearly circular and "flat" orbit, which many experts interpret to mean it's mostly undisturbed from its point of origin. It's a prime "fossil".
Pluto has a "disturbed" orbit such that its origin is currently unknown. Same for gas-giant moons. Pluto has also been turned inside-out, perhaps multiple times, by a still unidentified force. Ultima Thule is probably mostly as-is since formation.
Given lack of fast erosion from liquid water or significant wind (in a very thin atmosphere), whatever geologic process is smoothing out Pluto is happening quickly compared to other points of reference we have.
I use the example of Earth's geologic plates, but that's only one possible explanation. There's also speculation about freeze/thaw cycles of the planetary material and atmosphere (since it has an irregular orbit), movement of water-ice mountains, cryovolcanos, and other theories.
Some examples: https://www.nasa.gov/sites/default/files/thumbnails/image/du... https://www.nasa.gov/sites/default/files/thumbnails/image/nh... https://www.nasa.gov/sites/default/files/thumbnails/image/co... https://www.nasa.gov/sites/default/files/thumbnails/image/nh...