Balance doesn't matter for duels at all. You duel for fun, or to practice.
If I go up against a Warrior on White Mage in a duel, am I going to win? Doubtful, I suck at healer in PvP, but I can get some good practice in for proper PvP, where I'll have even more people on me. If I decide to challenge someone seriously, we can sort out balance ourselves by doing something like using them same, or similar, Jobs.
The only way balance would actually matter for duels is if they slapped Wolf Marks/PvP EXP on it and gave it its own tab in the PvP Profile to record wins and losses. That would be a mistake. Duels should solely be about simple, quick, fun/practice.
How is that a problem? Fun content is there for those of us who play to have fun, rather than grinding iLvls.
The only time the eventual drop off in popularity is an issue is when it is for required content (low level dungeons), or when the content requires a large number of players to even get started (Frontlines). Something which only requires one other person doesn't suffer at all from falling out of public interest. Not for those of us that actually talk to people in game and have friends at least. I very much appreciate that SE lets me play Triple Triad with friends, wish they'd let me do so in my Free Company mansion, but that's a different topic entirely. Duels are exactly the same for us PvPers. It's something to do when you're bored that doesn't require forming an entire party of queuing up for hours.
Nobody wants duels so they can duel all day every day. People want duels because it is a great (some would even say vital) piece of PvP content to do when they're bored. Given the only other PvP content involves us waiting for hours, I'd say a lot of us are bored and would like something to pass the time waiting. If I'm queuing for PvP, it means I want to PvP, that's why duels are the perfect piece of content to pass time waiting.