Bus is probably the most common way to go. I did it 20 odd years ago and apart from it's now a sealed road, the adventure seems to remain the same: http://www.ottsworld.com/blogs/bus-pokhara-to-kathmandu/
Flying is probably the most convenient. Kathmandu, Nepal (KTM) to Pokhara, Nepal (PKR) Non-stop flights: 12–13 per day, 0h 31m duration. Airlines: Yeti Airlines Domestic, Buddha Air, Nepal Airlines.
http://www.yetiairlines.com/ about 9 years ago