It really, really is.
I mean, the Fanatics' Tower is downright sadistic -- it's a huge, nasty, difficult slog, with no save points, ending in a boss who will almost certainly kill your entire party when you defeat him, and then, if you survive (which requires either Reraise or an extremely high-level party), makes you walk all the way down again, and not only that, but it offers no experience, so if you die you lose everything you've gained.
But, it's pretty easily gamed. You're not going to fall for that wipe-out-your-entire-party thing a second time, and players who know what they're doing can actually get in and out painlessly with a Moogle Charm and the Berserk and Reraise spells.
The Auction House, on the other hand, is bullshit.
The first thing wrong with it is that it is not a fucking auction house. It is a store with a randomized inventory where it takes an inordinate amount of time to buy things. Items go for the same price, every fucking time; you just have to sit through a goddamn cutscene before you can agree to buy them.
And the second thing wrong with it, of course, is the goddamn Talking Chocobo and 1/1200 Scale Airship.
Not only is it a store with a randomized inventory that makes you sit through a cutscene to buy things, but a very large percentage of the time (I'm going to say "majority", though people who've paid more attention to FF6's RNG can correct me) it hits you with a gag item that you can't actually buy.
This is, possibly, mildly amusing the very first time it happens.
For some reason, it is possible for it to happen a second time after that.
And a third, fourth, fifth, and seven hundredth fucking time.
And if you want to get two particular espers, or certain rare relics early in the game, you either have to study the game's random number generator to figure out how to get the things you actually want, save-spam until you get lucky, cheat, or actually sit through every one of the auctions.
Nice thing about emulation is that it makes it a lot less obnoxious, what with the ability to use a save state right outside the door and fast-forward to nudge the RNG. (On my last playthrough I was convinced that the item up for auction was seeded by your number of steps; this time I'm more inclined to believe it's time-based. I'm sure somebody out there has written an exhaustive guide, though I must admit I'd be more interested in just finding a hack that turns the damn thing into a store and lets you buy the things you want from it.)
Auctions -- actual auctions -- make a lot more sense in MMORPG's, where you're interacting with other players. So do extremely rare drops, for that matter. FF6 is less guilty of the latter than FF4, with its rare summons, Pink Tails, and such (though I've only ever seen one Economizer drop in all the times I've played 6 top-to-bottom and side-to-side), but there's slim damn reason for there to be an auction house in the game in the first place, and no reason at all for an irritating goddamn barely-functional store that pretends it's an auction house.