Overpowered on the forums wonders what the least popular instance is, and I'd say his guess of Blackfathom Deeps is probably pretty close-- it's a long run away for pretty much everyone but Night Elves, and at 25-30, there's so many more quests and things to do that BFD usually gets passed up. The other good guesses, I'd say, are the "old" late game instances like Naxx and LBRS. Unfortunately, while Blizzard tells us all about the most popular stuff in the game, they are pretty mum on what players don't like, for obvious reasons.
So how do you make an instance that makes players want to visit? Relmstein walks us through his idea of what makes a perfect instance ambiance: music, visuals, interactive features (the Chess Event is one of my favorite dungeon features, although almost all the dungeon dialogue "cut scenes" are fun for me), and memorable boss encounters.
But then again, BFD seems to have all of them-- it's a very pretty dungeon (I especially like the temple at the end), and while it might be a little short on interactive features, I really like the lore and the unleashing of the monster at the end. The last ingredient, I think, to a good dungeon, is just a storyline that drives you there. I'm sure Scarlet Monastery (except the Graveyard), and Deadmines are definitely among the most popular instances, and both of those have huge amounts of lore and mystery to make them interesting. Maybe if more players realized that Aku'mai was actually a pet of the Old Gods (or, you know, if there was a quest to kill him that explained that), BFD would see more traffic.