Are the Ludibrium and Command Center Warp Capsules limited for each account? Or is there a way to get more of each capsule?
You get a bunch of them from Omega Sector quests and that's it, I'm afraid. You could make a feedback thread to ask to make them repeatedly obtainable (similar was done with Bartol's Key Cards for Nautilus <-> Omega Sector warping) but I doubt it'll be implemented since it would make Eos Tower scrolls basically useless
I think these can be made more available, but the repeatable quest should be a little annoying to do and not award too many. The best use of the capsules is actually to skip the obnoxious Korean Folk Town elevator. I think some people don't know you can use them in KFT (not a glitch, KFT is part of Ludus Lake). Eos scrolls will not be irrelevant: sometimes you have business within the tower itself. And they are ridiculously easy to get from the rat quest at the bottom of the tower (don't bother with the one near the top).
