The reason why it's so much more difficult to orbit Pluto is that you have to take along all the fuel you need to slow down enough to get into orbit, and in order to take that fuel, you have to push it up to tens of thousands of kilometers per hour, which takes more fuel at the outset. And the faster you go, the more fuel you need to slow down.
It's taking the Cassini probe, which is to go into orbit around Saturn in 2004 and which is travelling at 30,000 kilometers per hour with respect to the Sun, 7 years to get to Saturn even after it was launched on the most powerful booster available, the Titan IV.
Pluto is 4.47 billion kilometers away, versus Saturn's 1.47 billion kilometers, three times as far. Keeping the Galileo probe functional since its October 1989 launch and its 1995 arrival at Jupiter has been an ongoing struggle, one that is not likely to succeed much longer, and that's over the course of a mere 13 years.
It took from 1977 to 1989 for Voyager 2 to reach Neptune to fly past it at tens of thousands of kilometers per hour using a gravity assist opportunity that comes along only once in 176 years.
The upshot is that with current propulsion technology, going into orbit around Pluto would take decades, far beyond the expected lifetime of space-worthy systems, and thus miss the atmosphere. Here's the web page of the Pluto/Kupier Express Mission.