I actually don't mind the "out-of-place-ness" of Omega's bosses anywhere near as much as Ivalice/NieR, because each battle is self-contained and you don't need the attached lore in the same way. Enter the battle, whatever weirdness of the setting is contained to that boss arena, return to reality at the end of it. It doesn't have to integrate into the main setting, and I can appreciate that as a way of including some bosses that people want to see, without trying to work them into the overall lore of the game.

I dislike Ivalice because it's too much of a lore dump via text rather than by playing and learning the world of a game as you go. The characters just aren't enjoyable or likeable enough from what we see of them here. It felt out of place at the time, and forcing too much of a new setting into the world rather than integrating into it and revealing new information about things established in the wider game (ie. Allag and Mhach in the previous raids). Though I suppose there's Goug, and whatever they're going to do with the Tartarus rift...

And NieR.... I've already written about this, but I dislike having a crossover as a permanent alliance raid rather than a temporary event. (Monster Hunter already did the permanent thing, of course, but there's nothing lore-shaking about that - just yet another dragon and a Hrothgar kid some kind of minor race from vaguely-elsewhere.) I don't know how heavily they're going to integrate NieR lore into the game because of this, but so far alliance raids do have further impact on the game world beyond their immediate story, and I don't like the prospect of this coming from a crossover with a non-FF game. It's not about whether the settings can be integrated, it's the principle of it - and what else they might cross over in future. (I think I'd be equally unhappy about this if it was a franchise I did like. Possibly more if I didn't like what it was doing to the other story setting as well.)