I don't disagree with that. I've always felt that a dungeon once finished should reward each player with enough money to cover repairs with maybe 0.5 or 1 wipe in mind. That way, once you master the dungeon, you will be making money, but excessive wipes will be costly as they should. Whether they do it via a gil reward for completing the dungeon or more even distribution of allagan pieces, I don't care.
But even if they don't, speed running like the AK runs are never ok, in my opinion. At lv50 if I wanna farm skins for LW, I have to deal with repairs too. Why don't I get the skins directly? If I wanna do FATEs for seals, I have to deal with repairs, why can't I just get the seals? Removal of speed runs is not slowing anyone down. Its making people take the intended amount of time to complete content. Its a MMO, what's the rush? Before the game launched people wanted long and tough endgame content. We celebrated when Yoshi-P announced that some dungeons will take a really long time. And now we wanna bitch about the fact that we can't skip the majority of a dungeon to complete it in 15 minutes unless we are rewarded for it on top of the actual goals. That is silly to me. I won't be opposed to more gil rewards for a dungeon and I'd actually welcome it. But its not a gimme more gil or I'm out situation. Dungeons are supposed to be long and are supposed to have trash. Not every encounter can be a Ifrit, Titan or Garuda.
When speed running is an option, people will do it. Human beings usually take the path of least resistance to every problem. Not only does that hurt new people who actually want to see the dungeon, it hurts the longevity of the game. If endgame is designed so the average person can get in 1-2 AK runs a night, allowing 5-6 AK runs a night is only going to make your content dry up. This is a MMO, content is meant to be repeated and take time.