It is indeed a problem when players are not completely dumb, as it wrecks bounded accuracy.
In my group there is a paladin, a rogue, a ranger and a barbarian. As you've probably noticed, they're almost all melee (some can fight at range but they prefer melee). Most of them have a way to negate all damage (or close) on Dexterity saves (Shield master, Evasion or Resistance). Against mental saves, it's almost always better for them to stay close to the paladin.
Auras are one of those things that make building challenging encounters a nightmare (along with GWM, SS, Polearm master, etc...). In our next game, I'll probably just remove them by making them "paladin only" or give the paladin's allies a reduced bonus (+1 to all saves for Aura of Protection, Advantage vs Fear / Charm for Aura of Courage and Devotion, etc...).
They also make magic items redundant. You just can't give a Cloak or Ring of Resistance to your players if there's a paladin in the group, because it makes things even worse. :/
I don't think it is being "a whiner" to prioritize story, intrigues or even detailling battlegrounds over encounter building. I paid 40 bucks to buy a Monster Manual, I don't want to spend hours modifying monsters to make them challenging, I have more interesting things to do, thank you.