Panniers are the only way to fly for me. The first year I commuted I used a backpack and hated that sweaty back feeling. Plus it just feels restrictive.

Panniers make it simple. A full change of clothes fits in 1 bag. I have a 2nd if I need to bring a lunch or something on any given day. And I usually keep it on the bike empty in case I need to bring something home from work.

A trunk bag won't fit a full change of clothes for me. My work shoes fill the whole bag. But they have their place too and I keep meaning to get one for when I need one....but thus far I've managed without a trunk bag at all.