Complete invisibility sounds nice until you think of shared things like mobs. Especially hunts. Are you okay with that A or S rank suddenly melting out of the blue without you even seeing player activity? O.O
And yeah, the duty part is absolutely insoluble. The only alternative is already illustrated by WoW, which does the opposite of FFXIV - and is probably 99% why Yoshi has it set up this way, especially when you consider 8 and especially 24 mans. I would actually not be surprised if a big reason why LFR is so worthless in WoW to the point of difficulty even getting a pop, is because of how robust their ignore system is: it does impact queue matching, in recent xpacs is even account wide, and people there will often blacklist for relatively minor breaches of etiquette (such as advertising your guild once too often in trade chat). Imagine trying to match an entire Alliance Raid under such constraints, it'd go from "Argh, I always get CT" to "lucky if you even get CT" overnight ...
Part of it I believe is actually the Japanese game culture, so I don't expect it's going to change at all. They maintain their do not party list via Lodestone IDs, and even though it is de jure naming and shaming, they do it on an anonymous board and it is so much an established part of the JP player culture that I expect anything that significantly changes this would be seen by them as far too much of a boat-rock.
Definitely this, I've seen entirely too many rated PvP games that become absolutely impenetrable to new players because of such aggressive filtering on the part of the existing ones. I'm not talking something like WoW, where you can try, but you're hopelessly outgunned (because of PvP having gear progression and the balance being so heavily gear based there, mainly), I'm talking like Guild Wars 1, where if you didn't play Heroes' Ascent when the game was new, good luck ever getting together a group for it. Even traditional games are often impacted, as anyone who's ever tried Spades or Sheepshead on the old Yahoo games could attest ...