Class Countering Conundrum

Hello fellow DMs, I’ve got a question with a bit of preamble, and it can be interpreted as a loaded one. I’m planning a new campaign for some college friends, and I’m taking this game as an opportunity to learn from my first campaign with these friends. Specifically, with bettering my combat as a DM. I had a Mercy Monk running roughshod over a lot of fights and I couldn’t figure out a way to stop them without being needlessly cruel with the monsters the gang was fighting so it ended up being on the easy side the whole time. 

My question is, how do I have a good counter for every class so I can be prepared and make the fights tough but rewarding for my players?

*IMPORTANT TO NOTE* I’m not wanting to be cruel and unusual to the party, I just want a way to have some more fun on my end, even if I will (ideally) end up losing the fights in the end.

...had a Mercy Monk running roughshod over a lot of fights

How does that happen?  I have a 7th level Mercy Monk and he is the lest effective fighter.  I don't understand how he can run roughshod over anything.

High level game (which was intended to be a shorter game starting higher but we didn’t even finish cuz school got in the way) with a Flurry of Hands of Harm. And an Aarakocra. With absurd chance to hit, I think we reached level 13 starting from level 10, and maybe the damage was overblown cuz a lot of fights were big, single-target things.

In short, monk destroyed a lot of single enemies and I want a way to make that feel more earned, among other things for other classes.

Flurry of Healing and Harm

11th-level Way of Mercy feature

You can now mete out a flurry of comfort and hurt. When you use Flurry of Blows, you can now replace each of the unarmed strikes with a use of your Hand of Healing, without spending ki points for the healing.

In addition, when you make an unarmed strike with Flurry of Blows, you can use Hand of Harm with that strike without spending the ki point for Hand of Harm. You can still use Hand of Harm only once per turn.

Sounds like someone either didn't read the feature closely or pushed a bad interpretation for the power- in either 2014 or 2024 the Flurry doesn't allow for you to turn every single hit into Harm, it just lets them stretch Ki by not paying for both the Flurry and the Harm. Mercy Monks only get a single Martial Arts die + WIS a turn from Hand of Harm, no matter what. It is a once per turn feature, and 11th level takes a moment to explicitly spell out that it doesn't supercede that.

...and I couldn’t figure out a way to stop them without being needlessly cruel with the monsters the gang was fighting so it ended up being on the easy side the whole time. 

It sounds wat you can do is to not have them do things they are not suppose to.  Learn about each character rules/features in the party and what they can and can not due.

"with a Flurry of Hands of Harm. And an Aarakocra."

Thats actually kind of an odd combination. Monk is melee, aarakocra is best suited for kiting around while making rabged attacks.

If they kite while doing melee attacks, every time they leave an enemy's reach, the enemy gets an opportunity attack. If you are letting them fly in, melee attack, and fly away without getting hit by an OA, then thats part of the problem.

Quote from SunIsGettingRealLow96589 >>

"with a Flurry of Hands of Harm. And an Aarakocra."

Thats actually kind of an odd combination. Monk is melee, aarakocra is best suited for kiting around while making rabged attacks.

If they kite while doing melee attacks, every time they leave an enemy's reach, the enemy gets an opportunity attack. If you are letting them fly in, melee attack, and fly away without getting hit by an OA, then thats part of the problem.

 
Eh- against anything with multiple melee attacks, risking a single attack to move out of their reach such that they can’t close the distance on their turn is a net gain on that front.

Unless theyre playing the Elememtal Evil Player companion version of aarakocra with a fly speed of 50 feet, they should have a fly speed of 30. 

If the tactic is swoop down 15 feet, flurry of blows, swoop up 15 feet (taking one OA), id say the enemies moat likely are devoid of ranged attackers? Level 10 and up, casters and other ranged enemies should be common

Quote from SunIsGettingRealLow96589 >>

Unless theyre playing the Elememtal Evil Player companion version of aarakocra with a fly speed of 50 feet, they should have a fly speed of 30. 

If the tactic is swoop down 15 feet, flurry of blows, swoop up 15 feet (taking one OA), id say the enemies moat likely are devoid of ranged attackers? Level 10 and up, casters and other ranged enemies should be common

 
Monsters of the Multiverse Aarakocra have a fly speed equal to their walking speed, thus scaling with Unarmored Movement. And no, it’s obviously not a flawless defense, but it does objectively reduce the number of melee attacks one will face, and those remain extremely common even in high tiers.

Wasnt disagreeing with you.

A lot of times when there is a "problem" with one player being a bit too powerful, a simple answer is to mix up the types of enemies. Like, most enemy groups operating at high levels have encountered plenty of flying targets, and would have ranged solutions. 

Can aarakocra Hover?  Make them Prone with a trident or spell, they fall for damage and are prone so advantage on melee attacks.