3 energy's, which is most valuable to refresh?

I would say it's still normal/hn. HN give you access to some of the best charcaters in the game you can't get elsewhere and to farm them you need to do refreshes. I honestly don't find the ship energy to be worth doing refreshes on. You should get enough each day to do the Sion node and maybe one other ship if you have any left to work on. Now if they were to reduce the cost of refreshes to 50 I'd say one or two refreshes would be worth it.