Yeah uh... I'm pretty sure most if not all of us can agree that Nekroz aren't exactly decently strong. There are other decks that fit that description that, while powerful, can't just generate advantage like nobody's business and easily find solutions to problems. Even if you didn't intend to use Fubuki in many or any duels, I doubt giving her a meta deck was the best call. Other than making the already mentioned power creep (and opening up opportunity for others to do the same), it's not going to sit well with anyone that there's a "police" character not controlled by the GM that's extremely hard to beat and can just stomp on everyone else.
As for Joseph... I don't think that "OCG/TCG" existed in the anime, so I'm curious as to why you even brought that into the RP :/. At least in my point of view, I don't think that something like that will be too difficult to overlook or change. Heck, once you change his deck you can just make something up by saying he had certain cards that until just recently, "weren't released from the OCG" yet if you still want to go with that.
I'll agree with you on that tag dueling thing, it really has made the RP slow down to the point where it'll die pretty soon if it isn't jump started. Perhaps a pseudo reset is necessary. We don't need to start from the beginning of course, we can just restart right when the Khan makes his morning announcement to the duelists. Other than changing the whole tag duels to regular duels, it'll give you more ease in remaking your characters and whatnot.
If we do that I can still manage to add in Ava and Lyall's duel against each other so that with it, things will go off with a bang.