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Pluto has the most eccentric (football-shaped) and inclined orbit of all of the planets. At the moment, it is actually CLOSER to the sun than Neptune, the next most distant planet in terms of average distance. This condition exists for about 40 years, or about 10% of its complete trip around the sun.

In addition, its current proximity to the orbital plane potentially allows a gravity-assisted path that could considerably shorten the travel time. This method has been used for other interplanetary missions several times in the past, with great success. The spacecraft is routed near one of the other planets, close enough that the planet attracts - and accelerates - it, cutting significant time off of the total time. Less time also means less exposure to failure.

These are not definitive arguments, but they are real.

Pluto crossed inside Neptune in 1979 and crossed back outside again in 1999. Due to the layout of their orbits, They will never collide. Look at this side view, it's pretty cool.