So, to start:

Those affected less: Ape (Rock is about half as effective as fists as fists have multiattack) Giant Ape (Rock is about half as effective as fists as fists have multiattack) Giant Frog (Can leap, but a flyer would just be further away) Giant Spider (Can web, but is much worse) Giant Toad (Can leap, but a flyer would just be further away) Those not affected: Blood Hawk Flying Snake Giant Bat Giant Eagle Giant Owl Giant Vulture Giant Wasp Underwater Creatures: Giant Octopus Giant Sea Horse Giant Shark Hunter Shark Killer Whale

These are all still entirely relevant. "Those less affected" can melee attack your melee attackers and ranged attack you just like if you were on the ground. Those not affected are irrelevant to this conversation. Underwater creatures are either fought underwater, where flight is impossible, or you are fighting them from above the water, in which case you are already out of reach.

Now then:

Awakened shrubs/trees, axe beaks, and every mammal you mentioned can be found in forests, where there is little to no room to fly and lots of cover to protect against ranged attacks.

Many of them can be found underground, especially the vermin; no room to fly there.

Any of them can be found outdoors during a storm that prevents flight.

Any of them can be found in an encounter with enough flying creatures to harass your Aarakocra sniper.

Any of them could be found outdoors at night so that the Aarakocra, who doesn't have Darkvision, can only stay within visual range.

Any of them could be found indoors, be they kept as a pet/beast of burden, or simply infesting the place as vermin.

Etc, etc.