So, I was wondering if I could put Nocheatplus on one Multiverse generated world, but on another keep it un-protected. If not NoCheatPlus, then a different plugin or strategy?
Excuse my ignorance, but what is Multiverse? And I don't see why not. I'm pretty sure plugins don't universally effect worlds.
Take a look at their wiki. This link should explain everything you need.
From my knowledge, Multi-verse provides individual folders for each generated world, so you can put NCP in just the world you want it in. If that doesn't work, try install plugman to manage your plugins.
Josh | Media Editor: Photographer & Videographer | Advanced Minecraft Server Administrator
"Only god knows what we're fighting for!"