I feel that the loss of Qwilfish is going to hurt the game a lot. Qwilfish was relied upon to take on a multitude of roles. Absorb Toxic Spikes, set up Spikes or Toxic Spikes of your own, neuter physical Attackers, check Fighting-types, cure cancer, create world peace, Qwilfish could do anything! In all seriousness though, the loss of Qwilfish is going to leave an unfillable void. I mean, who else can do all that Qwilfish can do? Roselia can get up Spikes and Toxic Spikes while absorbing Toxic Spikes, but it wishes it could check nearly as many Pokes as Qwilfish. Lets not even mention Garbador.
Krookodile too, is going to be incredibly difficult to replace. I mean, it is one of the best Ghost killers in the game. Having a Krookodile remove Rotom and crew from the game so Medicham or Hitmonlee can spam Hi Jump Kick, or Porygon-Z spam Tri Attack, is invaluable. Honchkrow can theoretically pick up the slack, but its better off sweeping on its own, not to mention Krookodile has STAB Earthquake too. While its influence on the metagame isn't as great as that of Qwilfish, Krookodile's presence will be sorely missed as well.
IMO, RU is balanced at the moment, but with the metagame still growing, there are still a ton of innovative sets on the horizon that may make or break (break can be interpreted as becoming broken or becoming useless) a Pokemon. Furthermore, who knows how things will shake up with Qwilfish and Krookodile, and perhaps even Honchkrow gone. The potential for a the metagame to be turned upside down with these changes is, I would think, enough reason to hold off on "is the metagame balanced or not" debates.