These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Awesome Ego: Saber. She's got a bigger ego than Shinji, but rather than annoying, it just makes her awesome.
And now, the ORIGINAL king is here. Even more awesome than his F/SN counterpart.
Fetish Retardant: Saber's see-through skirt is not titillating so much as pointless and hilarious-looking. Similarly, some shots of the new costumes in CCC cause her and Caster to look like they have Gag Boobs to the point of becoming unappealing. CCC takes it Up to Eleven with Sakura's various "clones," particularly Passionlip◊. And then there's the final boss, whose special attacks basically revolve around spreading their legs, summoning planet Earth from their vagina, and attacking you with it. Regardless of whether it's supposed to be Fanservice or actually intended as Fan Disservice, the whole thing ends up looking rather comical.
Foe Yay: Leo, with the protagonists, especially after they beat his brother and when they're both in the finals. He's rather excited at the thought of fighting them.
Leo: *Giggle* "I'm as enamored with this feeling of competition as a little girl is with a fairy tale."
Along with his Master noting the protagonist's "rump" (though in her case it's more because she wants to eat you), the way Vlad talks about Saber, Caster, and especially Archer more than implies this.
There's some between the protagonist and Julius, too. Seeing as how he comes back as a virtual ghost just because he can't stand the thought of losing to you, it's pretty evident. And it's not one-sided, either. You end up either crying or holding his hand as he dies. If you choose to say that you wanted to understand him, the narration notes:
You: "Somewhere deep within that fervor, I uncovered my enchantment with this steely killer."
Fridge Brilliance: Why does Alice's Caster's Reality Marble cause a Loss of Identity? Because Caster, whose form changes depending on who summons her, has no identity of her own!
Genius Bonus / Bilingual Bonus: Red Saber calls her master "Sousha," in game this is translated as Praetor, however a literal translation would be Player, as in one who plays music in theatre. Musical theatre being something of an obsession of hers.
Ho Yay: Some minor examples between a male MC and Archer, such as Dan's Archer making pointed comments about 'domestic strife' and the Week 7 Day 2 scene still playing out like a Love Confession, though it's downright mild compared to the below; possibly Foe Yay between a male MC and Julius, if you've got your Shipping Goggles on. Ronnie's Lancer, on the other hand, is as forthright with the Ho Yay - upon being confronted with the playable Archer - as you'd expect from his other lines.
Lancer: "Is it not fateful, stiff-backed archer?"
Lancer: "That noble stare of yours outshines the moon. You are the Apollo that I have been searching for!"
Lancer: "I long to pierce that supple body of yours with my spear. You compel me, you, you— You supremely gorgeous creature."
While not to the extent as the female MC, the male MC has been paired up with a lot of the other characters as well.
Les Yay: The female protagonist reacts very similarly to how the male protagonist acts when it comes to interacting with other girls, including being awed by their beauty. The scene in which the girl you saved gets jealous over the other girl feeding you lunch plays out exactly the same with a female protagonist as it does with a male protag.
Both the playable Saber and Caster fall in love with her. Caster even declares her to be her husband if you choose the right options, just like with the male protagonist.
Lil' Ronnie is painfully annoying to listen to. aNd rEaD.
For Fate/Extra CCC, Passionlip is already receiving flak based entirely on her physical design. It's mostly on the fact that in the original Extra, the game had fairly good and interested character designs. Passionlip to many represents a blant attempt at appeasing the people who felt that Extra wasn't ecchi enough like Fate/Stay Night was.
The Untwist: If you read through Caster's skill list in her information section, you can learn her true name (which is regarded as a very important subject) on as soon as the first day. You'll still act as if you don't know it when she reveals it, of course. This is very likely to be a goof with the translation.