Two reasons, actually.
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It’s not their preferred preparation. All the replicated food is based on a pattern from an original recipe. It’s not adding flair or anything, it’s literally a copy of a dish made who knows how long ago. And that’s where the next reason comes from:
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Imagine eating some spicy pepper dish from, like, the 1940’s vs the same dish made today with spicer peppers. It wouldn’t be as spicy eating something that wasn’t, at the time, really selectively bred to be more spicy. If the recipe for the replicator is, like, hundreds of years old it would probably not be as potent as the same dish made with real ingredients.
I can imagine that the characters that have expressed disdain for replicated food probably get hit by both of these. It’s not the way they would preferred it to be made, and it’s also like eating vegetable jello salad in 2024.
One more reason: The dish tastes exactly the same every time. No variation at all.
But when you cook real food, there is always a little variation because the ingredients are usually always slightly different (vegetables more or less watery, meat more or less lean, a little bit more or a little bit less salt or flavouring). It’s one of the main skills of a really good cook: To perceive the subtle differences during the preparation and to bring out the best possible taste incorporating the differences.
There’s no technological reason why there couldn’t be hundreds of versions of each exact dish. In fact they could’ve even had a simple variation program so that every time it’s made it comes out a bit different
I mean, that is conjecture right? With how much the real military puts into food science, I could imagine that there’s a Federation food science division that could easily make a dish from scratch a number of times and store each attempt’s pattern as a random variation that gets distributed out to the fleet.
When I was in, they put zero thought into it other than “needs more calories” and “make soldiers poop less.”
Considering a post-scarcity universe where the machines they’re working with can take even those considerations away from us (IIRC the replicators automatically do adjust nutrients/calories per-person per-meal). I think after a while, someone would’ve just… Gotten bored and futzed with it. I’d also assume consumers on earth to contribute to the databases. Heck, there could be a whole food influencer culture thing going on. “Oh man, you haven’t lived until you’ve tried ‘eggs, scrambled, variant 37578a’!”
I think we have something contemporary to compare this sci-fi scenario with: recorded vs. live music (especially now that we can keep making exact digital duplicates as nauseam.)
When you play a CD, it sounds the same each time (ignoring things like the equipment you’re playing through, the room, the ambient noise, etc.). Usually, the studio recording is the best, most pristine recording of a song you can get.
But when you see the original artist performing the song live, it’s different! A good performer will make you feel like you’re experiencing something special. And the little variations, and even, imperfections, make the song even more compelling!
It’s the CD recording of the song bad? No. It’s perfectly serviceable. It might even contain things that can’t be performed live. But it’s the same each time. And for some people, that makes it less desirable, and live performances, with all their deviations and mistakes become more desirable.
And going back to replicated food, apart from Eddington and grandpa Sisko, I don’t remember anyone else saying replicated food was bad. Just less desirable. And even Eddington grudgingly admitted that the TV dîner he was eating in the shuttle with Sisko wasn’t that bad.