Why are these abilities considered "banes" of "cool" dungeon design in the first place? Because you get to skip a jump or climb check at the cost of a resource?
/snip
For me, the problem is twofold.
1. The casters simply negate the skill users. What's the point of having a skill monkey character when two or even three of the characters in the party can simply bypass whatever skill check through magic? The monk example is a perfect one. The monk had actually spent character resources to be able to do the wire-fu thing. Very cool. Very in character. Rule of cool and all that.
Then the paladin says, "hold my beer" and teleports to the top of the roof, no checks, no chance of failure, no drama and about as interesting as soda crackers. I mean, do you really picture, in your head, when thinking about paladins, Portapaladins bouncing around the scene? I know in our group, we had a fighter and a paladin, and the pally almost always got into a fight before the fighter. Bonus action teleport, poof, he's in the thick of things. Gee, the fighter can burn his Action Surge for extra movement, but, he's only got that once per short rest. That 8th level paladin has what, 3?, second level spells.
2. On your second point about running out of resources, well, there's a couple of things there. Firstly, the casters get SO MANY resources. Sure, Teleport might be a bit of a bit resource wise, but, the lower level stuff? Not so much. And, secondly, it starts the whole 15 MAD cycle off with a bang. The party is all (or mostly all) casters. It's in all their interests to stop for long rests and get spells back. IME, it's not unusual for 3/4 of the party to be long rest based, which means that 3/4 of the party wants to stop at the same time.