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.
Depends on the trip and the mass of the spacecraft. IIRC, Prometheus would take years to get to Jupiter, even though New Horizons will reach Jupiter in one year. The advantage to Prometheus, besides having almost too much power, was that the ion engine would allow it to change orbits with regularity.
Remember, assuming constant acceleration and negligible starting velocity, travel time = SQRT (2*distance/acceleration). If we had Prometheus-level technology now, we *might* be able to get to Pluto faster. However, since we've dawdled instead of developing ion engines further, we're forced to use chemical rockets for the forseeable future.