The problem isn't that these things exist. It's that they've been done poorly, in some cases, like the disaster that is PvP gearing, or Titanforging, or Warmodes.. Or, that they clash with other systems, like M+ and raiding.
Though, largely, it's because they've been poorly designed or implemented. There is no system currently in WoW that is inherently bad (In my opinion), only systems that are badly made.