No, don't take them over training potions and command flag frags. Those two things should be your #1 priority to collect. Also don't pick advanced vials/protections over refines. The only thing I'd pick them over is Mt. Myoboku stuff.

Also, there's no real reliable way to get the normal protection vials from events. They are only in them rarely and there's pretty much no other free way to get them. It's so frustrating and a lot of people have asked them to put them in the moon scrolls shop but who knows if it will ever happen. But yeah that's just how it is right now.