This question asks about how can a DM create suitable challenges for players with Aarakocra, who can fly at will. The question refers to challenges like pits and towers, which the Aarakocra can simply fly over. The answers mostly focus on combat (flyers have no cover, are easy targets, etc) and on the premise that only that player-character can fly, so he can climb the tower or fly over the pit, but the rest of the party is left behind.
However, either I have some misconception about flying or the answers have not taken something into account. I feel like I understand exactly where the OP is coming from, because I have made many dungeons with exploration challenges, pits, wells, vanishing walls, barriers, broken bridges, etc, that make my players come up with creative ways of bypassing them. Either by casting spells, or by using resources, or rolling for athletics and acrobatics shenanigans. My actual problem (and I believe the OP's as well) is, if we have a permanent flyer on the party, he can always just carry everyone over all these challenges.
Sure, there could be enemies someplace looking at the skies waiting to check if an Aarakocra is coming by, or enemies will eventually know the party has one, but that doesn't ring well with me. The party is low-level when this is an issue, they won't be that widely known. Enemies may vary, the don't always face the same group who will know that the party is coming with flight. Low level enemies are dumb, they don't account for possible means of entry from the sky.
In dungeons, specifically, if there is some pit which the party should make checks to go over, or use spell slots or shapeshifts or whatever, an Aarakocra just negates the resource usage for this, I might as well remove the pit and move along with it. Even if I had enemies on the other side waiting to attack possible Aarakocra flyers, the party would either not go that way (as they couldn't go ever over the pit while being mercilessly attacked by out of reach enemies) or they'd kill the enemies first from afar, and then have the Aarakocra carry them over.
I can maybe imagine that a flyer couldn't carry the party members over challenges, but I don't recall reading anything of the sort in the rulebooks. As far as I can tell, maybe he'd move as in difficult terrain, but that was it. So once more, how is exploration any challenge for a party with a permanent flyer, focusing primarily on the issue of that flyer being capable of carrying everyone over everything?