In the order that I did the content.
Werlyt
Somehow, I'm not surprised Allie ended up being the one to make it out of the whole mess alive, though I was honestly a little concerned they were just going to leave her catatonic at the end.
I think I'm mostly satisfied that Valens met his end in a manner fitting for the wrongs he had committed. I definitely didn't expect that twist that he decided to just ditch his original forced Oversoul scheme in favor of making Alphonse himself the core for the Diamond Weapon which backfired horribly as it mostly allowed the orphans' scheme to play out as they had been hoping it would. I had considered the possibility of Diamond being operated as a tandem machine by both of them in advance, though, and that kind of came true in a twisted way.
I am curious in what role Gaius will potentially play in the future now that he's committed himself to helping Werlyt establish a new governance for the time being.
Nier
Err...I really don't have much to say about this one.
The mechanics on some of the bosses were interesting (The third boss was the star of the raid IMO), but the actual story just kind of ended with a whimper and the main point that were brought up (Namely the how/why of the dwarves crossing over into the other world) didn't actually get explained.
I'm not really expecting anything noteworthy to come from the drip-feeding of story we're getting from the weekly quest, either.
MSQ
I never really considered the possibility that Tiamat herself likely had been tempered by her proximity to Bahamut. It was interesting to learn that her brood also had a friendly relationship with the peoples of Meracydia for a time before the Ascians and Allagans ruined everything, and having her finally break free and resume her life with a positive outlook was really satisfying after regularly passing her on my trips through Azys Lla.
The dungeon was really good and made me wonder just how big of a conflict we'll be facing in 6.0 with the sheer amount of tempered comprising the Telophoroi's forces.
Mu suspicion about the towers being powered by the tempered ended up being true...though I'm curious as to what the heck they intend to do about them in the long term if they're basically primal factories. as they can't be ignored. I'm glad Arenvald survived the incident despite the numerous death flags he raised in the brief time before his departure, though.
it seems like we're finally going to get an answer to why Hydaelyn has been all hush-hush with Krile being the one to finally question why she hasn't spoken for so long, and the mention of possible interference does make me wonder what's been going on since we last spoke.
Lastly, I'm really curious about what the "you-know-what" Fandaniel mentioned is considering that the Garlean royal palace is now basically a much bigger version of the towers we've been seeing, which would imply it's meant to be used in the summoning of something much more unpleasant. My first thought was Anima, though what role it would have to play eludes me.