I definitely agree with you that the ghost towns are a big problem right now. My personal favorite solution is functional structures – in the name of blatant self-promotion, here’s an old post with a bunch of ideas along those lines:
But, of course, that isn’t the only solution, or necessarily even the best one. My inner builder is shrieking in agony at the thought of fewer plots, but you could well be right that making them a tradeable commodity would help. I’d buy em! 
The other…well, not a problem, but certainly a contributing factor, is that the mining/crafting/building aspect of the game is much more complete, at the moment, than anything else. Right now Boundless is a building game with MMORPG aspirations. If you aren’t at least somewhat interested in building/crafting, there isn’t much for you to do in the game – so it’s like having an IRL city populated entirely by architects. We don’t have anyone to inhabit the endless things we build.
I’m hoping this will change as the combat system gains complexity, and the game can attract and keep people who prefer fighting to building. But I don’t know what the devs have in mind, for 1.0 or afterwards!