Okaaaayy so I had feared there was residual dirt in my savefiles, and started a new character to play up to when them Daedra wanted to chat. Lo and behold, crashes again.
I also tried to just run without SKSE but scripts still run, mostly.
Tried to disable everything and enable 5-10 at the time, turns out this is the culprit
http://www.nexusmods.com/skyrim/mods/65678/? Mythos of Bledaen
Would've never suspected that! The author says it's possibly due to load order but didn't offer a possible conflict.
So, the issue was incorporeal voices that still have a world trigger, such as Clavicus Vile (statue), Hermaeus Mora, Augur of Dunedain, whispering doors.
Meridia, Sheogorath and such are OK (they are actual NPCs), so is Mehrunes Dagon and you can't actually trigger him either - he'll speak to you.
I'm just glad it wasn't one of the gameplay changing mods that I'm rather attached to, and I got to try running away from Meridia and watch her catch up in the middle of the sky, so that was kind of fun.