It's usually faster to buy a ticket from an airline office rather than a travel agent. The departure tax on domestic flights is d15,000. Bus travel is definitely uncomfortable and frustrating, but if you treat it as a social function rather than a means of getting from A to B, you should survive with your sanity intact. Most long-distance buses leave early in the morning, so it's a good idea to buy your ticket the night before. There are express buses, but few are really fast.
Public minibuses suffer the same drawbacks as public buses.
The alternative, used by many foreigners, is to charter a minibus. They cost more but they are much more comfortable. You'll find people taking bookings in popular tourist destinations. Budget hotels and cafes are the best places to start looking. Train travel can be even slower than bus travel, but it is more relaxed and you're likely to have decent legroom.