The issue of "empty zones" as you call them, is entirely caused by "Expansion" based games. I mean, these zones would be even more filled if new ones weren't added for story content every expansion. Imagine if they had to fit everything from HW to SHB into the ARR zones instead of adding new ones? There's also the fact that FFXIV is a game where EXP is generated primarily from quests and instanced content, as opposed to mob killing in open world areas (mob killing for EXP would allow them to vary the enemy level in many zones to accomodate leveling groups for example)

In short, this kind of thing happens in games of this style. As a gatherer, I've visited pretty much everywhere, and i always run into a couple of others running around. It's certainly not completely empty, but then I also realize what type of game this is, and due to that I don't expect a populated open world.