Keep in mind ion engines are fuel efficient, not fast. It took SMART-1, what, a year to hit the moon? The fastest way to get to Pluto before the atmosphere freezes is to go the conventional route.
Ion engines shine on longer missions where their steady acceleration is of more use. The ESA moon shot was just a way to test fly their version of an Ion engine.
The real major advantage of Ion engines is in their efficiency. They are ten times more efficient than chemical rockets meaning far less propellant and larger payloads. Even if they took longer the payoff in more science per probe is worth it in spades
The propulsion for the Pluto mission has alread been selected and as you suggest it's going to be conventional with a huge kick from an Atlas rocket and a Saturn (Jupiter?) gravity assist. The power supply will be radioisotope thermoelectric generators which rely on nuclear decay. I think it's slated or launch early next year.
You misunderstand the physics. Over the long travel time and distance to Pluto, the effect of nearly constant acceleration adds up to a LOT of velocity. SMART-1 to the Moon was a short distance with a lot of time just going for orbit insertion, not point-to-point travel. Prometheus and others of its type will make long-distance trips in very foreshortened times.