HMs don't make much sense at all.
-Why can't you walk past a small, waist-high shrub? Why do you have to cut it down? And why does it grow back when you walk out of sight of it? And for that matter, why do you have to use the move Cut to cut it down? My Aegislash is a huge steel sword. Couldn't it just cut the little bush down? And what about my Typhlosion? Couldn't it just burn the bush down? And wait, I have a Pidgeot! Couldn't I just get on it and fly over the bush?
-Why can't you climb over a boulder that isn't even as tall as you are? Why do you have to break it? How does it regenerate after you smash it and walk away? Is there a Golem living in the cave that places boulders in the same spots over and over again when one is smashed?
-Why do you have to move other boulders? Couldn't you just smash these as well? Wait, these aren't that big either! Couldn't I just climb over them? And how do they move back to their original placement when I leave the cave? Does Mew appear and teleport the boulders back to their original locations? Why do I need Strength? Why can't I just tell my Machamp to push the boulders? He's strong enough, his Pokedex entry says he can move a mountain! Are these boulders made of some unearthly super-heavy substance that can only be moved with a specific move?
-Are flashlights really so expensive that I can't just buy one for when I go through Rock Tunnel? Why does my Pokemon have to light up the dim area? Why can my Oddish learn Flash? It's a little weed, it's not bioluminescent at all! Wait, it's called Flash, so does that mean it's just one flash of light? But that wouldn't light the cave up for more than a second! So is it a series of flashes? But what if I have epilepsy? Do I have a seizure as I walk through the cave? Apparently it's a common enough problem, it got a Pokemon episode cancelled! And why do I have to learn Flash? I've got a Chandelure, doesn't that emit light? Can't I just let that out of it's Poke Ball?
-Why can't I fly to an area I haven't been to yet? Does my Pidgey refuse to land anywhere it's never been? And don't say yes, because I can just catch a new Pidgey and have it fly somewhere I've been, but it's never been! And... wait, what? Pidgey? But that thing doesn't even go up to my knee! How can it carry me? And how is that safe? Where do I sit on my Pidgey? Do I hold on to it's legs? What if I slip off? What if my Pidgey gets tired from carrying a human being 6 times as large and over 35 times as heavy and comes crashing to the ground?
-Wait, I can't swim? Can't I learn to swim? No? Okay, what Pokemon can surf me around? Okay, let's see, Lapras, Wailord, seems fine, wait a minute, Sentret? Tyranitar? Aggron? First of all, Sentret is nowhere near the size of a human, and definitely not as strong. Is it buoyant? Do I hold it like a life ring? And Tyranitar? But that thing is weak to Water-type attacks! How could it take a whole sea of water? Wouldn't it be downed in a few seconds? And Aggron? Aggron can't take one Water-type attack without being KO'd! Plus, it's made of metal! Wouldn't it rust out?