There are lots of games that you should only add the expansion for after getting very familiar with the base game, but I can’t fault them.
The only expansions that come to mind right now as being detrimental are for games that only work because they are very simple. So, Power Up for King of Tokyo is an example.
I would say every good game can and should get away with zero expansions. And now we’re at a point where expansions are more than base games I’d suggest it’s better to buy a new game.
Warriors (not that anyone is ever likely to get a copy) was completely ruined by the Dragon Hordes expansion. So bad that I threw it in the bin. So long ago now that I can’t fully remember the details, something about extending the game and messing with power balance and removing the fun from the game. It is legendary in my group of the last 15 years as the exemplar of bad expansions.
Keyflower probably fits with what @Benkyo was saying. The expansions may be good but you need a group familiar enough to manage the wrinkles and understand how the points the new things offer will score. I’m not there, so I won’t put them in again.
Bora Bora felt more tense and interesting to me without the Orange God tiles. Managing your dice rolls and balancing green, blue and white gods was much more interesting than having dice mods for lower cost.
Celestia’s expansion messed too much with the core calculation for me. Made the game less fun as the hidden cards were too extreme rather than ‘I did have 2 pirates and wild for this 3 pirate roll’!
I’m going to throw Tsuro of the Seas into this category, as if it were an expansion to Tsuro, because you can play TotS using the original rules, but if you include its new elements then it ruins the game. It’s quite impressive just how comprehensively the designers have failed to understand what was good about the original (IMHO of course). There’s a third game in the series now, which doesn’t sound much better to me.
Thinking about it, as much as I love it with the expansions (the tiny airship!!), it definitely makes things more confusing for anyone not as familiar with the game.
Lots of “Hey, can I look up what this card does?” passes rulebook “It’s not in here?” passes expansion rules “It’s not in here either …” passes other expansion rules
More games need integrated rulebooks. (I’m working on writing them.)
This makes me so sad. It’s exactly why Celestia doesn’t hit the table more often. Even the base game has a “what does this card do? If I ask, everyone will know what I have. They should have printed language-specific cards. I guess I’ll just look in the rulebook and everyone will know I have something weird” problem
Or at least some kind of handy reference that you can glance at.
It wasn’t my intent to find fault there, just another (personal) spin on a game being “better off” without the expansions. In my case, with the frequency it gets played, it’s very unlikely I’ll use the extra stuff to augment my game, and I knew that going in. I’ve got a lot of extra stuff that’s basically relegated to the bottom of the box, and given how many people bought into the all-in pledges or big box option (versus those who play regularly), I’m guessing I’m not alone. Thankfully there’s a lot of cosmetic junk there, and it all fits easily in the main box anyway.
But if we want to stick to the purest definitions, the Squirrels and Conifers expansion was created to a) help colourblind players pick out food cubes more easily, and b) cater to fans who perceived a food shortage problem in the base rules. Setting A aside for its intended users, I have no problem with the rules as written and find the option wholly unnecessary.
Gosh, I can’t think of too many. You obviously don’t want to play Arkham Horror 2nd edition with all the expansions mixed in - even with Miskatonic Horror, which is specifically trying to address the issue, there’s a lot of expansion-specific mechanics like the King in Yellow Act mechanic that go nowhere if you’re wading through a ton of other expansion cards along the way. But you still benefit from owning the expansions, you just should only play with a couple at a time. I guess you could argue that you don’t want the Black Secret (or whatever it’s called) expansion for Ghost Stories because it turns the game into a one vs many and that’s less fun…but I think that’s mostly just a “does playing this one vs many sound fun?” check before you get it. The first Race for the Galaxy expansion added rules for invading other people’s planets that are, IMO, not fun, but they’re also not integral to almost anything you get in the expansion and can pretty easily be ignored.
The one example for sure I can come up with is this: Machi Koro’s Harbor expansion. Now, i don’t think I would like base Machi Koro either, so, grain of salt. But Harbor adds two things that are just painful. 1) two additional buildings you must construct to win that require accumulating substantially more cash than the base ones. 2) cards that let you steal money from other players (I believe this is new in Harbor, I may be wrong.). This combination led to a horrid, endless series of turns where money sloshed around from player to player such that nobody could really accumulate money between turns, and taking well over an hour to land with someone at the right point for them to actually be able to construct the final building and win. That player happened to be me, but I sure didn’t feel I’d earned it. (The game took over 3 hours, which was also ridiculous, but I think it was primarily constant unending theft for the last hour-and-change.)
Machi Koro base has the red cards which are basically “take cash from the player who rolled this number”.
I think there are at least three different classes of expansion:
I think it’s just that Harbor added a bunch more and a couple purples that do the same. But in a game where you win after just the base game landmarks, they wouldn’t be so bad. It’s having to build up to the extreme cash-in-hand levels of the Harbor landmarks that made it awful.
I bought a promo expansion for nmbr9 which gave each player a special piece unique to them.
Totally stole the fun of finding out how someone else solved the puzzle as the extra piece added too much differentiation between players.
I have a mini expansion for Camel Up that adds a “referee” camel, which allows you to unstack the rest of the camels. This makes the game much more boring 
Most of El Grande’s expansion modules are rubbish except:
I have heard awful things about Shogun’s expansions, and having played them… I am not a fan. I love the elegant chaos of Shogun, and the expansions add piles and piles of fiddle to a very elegant “wargame” (which, brilliantly, isn’t a wargame, it just LOOKS like a wargame and has some wargame-y elements). But I get why some people might like them more than me.
Twilight Imperium 4th Edition’s biggest upgrade was speed. The whole game could be played at a blistering 30-45min per player (6 players in 4 hours! Sign! Me! Up!). Prophecy of Kings adds a tonne of interesting new races, fascinating new mechanics… and drags that time back to the 1-1.5 hour per player length. And, unlike the old expansions, you can’t pick-and-choose elements. It’s a take 'em or leave 'em. I love 'em, but man, I wish you could pick a few to use.
Terraforming Mars has some very good expansions (Prelude!), but gosh Venus Next is awful. Longer, but not better. Just longer.
Going real old skool, Thurn and Taxis is a great little Ticket-to-Ride-like, but the expansion just messes everything up. Too complicated, too weird.
U-boot comes with an $80 “all resin upgrade pack”, and gosh is it ever a waste of money. You get like… 10 pieces of resin? Nice, sure, but at $8/pop, no way.
Oh, and this is really petty, but I dislike that one of the new Lord of the Rings: Journeys in Middle-Earth expansions lets you play as Gandalf. Gandalf! Slumming around like a common burglar! I’m sorry, I know lore=/=game, but Gandalf is like a freakin’ demi-god. He should not be on the same power-level as Bilbo or Gimli.
I didn’t know it had an expansion. Loved that game, such a shame is out of print.
I think that crosses the line that on BGG separates “expansion” from “accessory” - similarly the Firefly resin ship models or the Colt Express mat, which make no difference at all to gameplay but render the game prettier.
An exceptionally good point. In my head they’re all jumbled together… we sell them in the store as “expansions,” but our systems is pretty crude when it comes to inventory control (hobbled together by two brothers as they worked for over 30 years in the various industries… sports cards to pogs to toys to games).
Okay, how about the interesting-but-gosh-expensive Colt Express Bandit expansions? Little AI controls that each let you play against 1 Bandit controlled by a deck… each for about $8? Buying all of them actually costs more than the game and gives you a stack of cards about 1cm high, total.
For their intended purpose (fill in one empty player spot) they’re a bit rubbish. You can however use all of them together, against the explicit instructions of the designer, for a solo game with a player Marshal.