The Crystal Tower is still ran regularly. It can take a while, but Wondrous Tales alone, plus ingredients for Anima Steps seem to encourage people to queue up. I expect the same to be true for the Sky Pirate raids, and who knows, maybe at some point we get a Alliance Raid Roulette.

Alexander may be harder, but I still see people running Bahamut once in a while, so I bet that may also still be a thing. EX runs may be slow queues in duty finder, you will be the bane of mentors, but those are best done with a party finder anyways. I hope they never give strong incentives to do EX trials, though. I don't have any fun doing those.