So your point is that there shouldn't be a playable meta without a ban tier above it, right?
iirc, we had a similar discussion in rby2k10, since people decided to move some overpowered BL pokes to OU despite not having enough usage to be OU.
So the main question is imo whether tiers should be based merely on usage, having a ban tier for each usage based tier (UU has BL, OU has Ubers; but BL doesn't change even if there is something clearly overpowered), or the tier "playability" should be the main concern when making tiers, and, therefore, OU should also act as a BL ban tier and UU as a NU ban tier.
To avoid "waters countering waters", the only solution is imo banning amnesiers, as they are only walled by other waters. This would imply banning Vap as well I guess since it would be clearly overpowered then; in the current meta Poli/Golduck make Vap less overpowered and vice versa. Making this change would turn into a completely different meta though; better meta or worse meta is subjetive.
Charizard is much better that other fire types, yet it's still pretty bad in UU. Without Charizard, fire types would NEVER exist in UU.
Lastly, being overpowered or not, it's also very subjetive, and if one poke is good or bad for the meta; or if that meta with A, B and C banned would be better than this one, even more subjetive. Think of GSC Snorlax, or just RBY Tauros. There will always be one poke better than the rest, and then the second best etc. Creating a meta where everything is equally good is impossible, and would be a stupid meta imo.