In the nether, I was unable to do faction commands. I'm not sure if this is the case for other commands as well.

This is intentional. Nether and the end are excluded from the factions plugin.

I feel stupid now.

Actually though, there are areas in the nether at least that have been claimed in clans. I assume that was before this decision was made. Will they be wiped?

Yes

I like that.People in the nether and really in the end are herd to get and never leave their base

I'd like to report a bug. Some people can fly so clearly there is an error in permissions since this is hardcore PVP.

Do what's right and allow no one to fly, and that means no option to fly.

This is not a bug, currently Staff can fly. No members.

That is what I am implying.

I was concerned with this as well myself. I am willing to allow this ability for the Staff considering the fact that at times, this could enable them to complete their duties more effectively. I had a discussion regarding this and had also voiced my concerned.

Thus Moderators/Staff can keep that ability with the simple tolerance 0. It should never EVER be used to promote an advantage during actual "gameplay" but only used to assist other players or perform moderation tasks.

The Nether and The End shall be reset at some point and time in the near future to mitigate any Faction Claims which could have been made before the decision to remove Faction Action in those worlds.