In the entire franchise? Keep in mind this is just my opinion.
-If you accidentally kill enough hostages in MSX Metal Gear, the game becomes unbeatable. Bad game design.
-At the time, when Metal Gear Solid 2 did the bait and switch with Snake & Raiden, I absolutely hated it. All the trailers showed only gameplay of Snake. When the game transitioned to the Tanker chapter, I was like, “Wow, a different character to play, cool.” Then when I saw ‘Iroquois Plisken’ I thought, "Okay, at some point I’ll switch back to playing Snake.
The sad thing is, I didn’t really mind Raiden at all. Seemed to play the part of an inexperienced combat guy then grew into it. Didn’t even mind the Emma hand holding/swimming mission, though I was frustrated with it at first.
-Speaking of Metal Gear Solid 2, the ‘I had a relationship with your mother’ line from Hal was a bit, jarring.
I was tearing up at Emma dying, felt so bad for Hal, then “Oh my god this is so sad - wait, you did WHAT with her mother?!” Just seemed totally from left field. I imagine it was intended to be a surprise, and well, it accomplished that mission admirably.
-The nut grabbing in both MGS 2 and MGS 3. Seemed both out of place.
-In MGS, the mines the game DOESNT tell you about. That was annoying.
-MGS4…, honestly Snake should’ve offed himself. The daddy reveal at the end felt so forced, so tacked on. Really felt like Konami pressured Kojima not to kill Snake. David Hayter said it best.
“I never believed for a moment that Snake would hesitate to do it. He’s the one guy that knows that when it’s time; it’s time.”
Nanomachines are a gigantic plot hole. At the end of MGS, Campbell said:
The batteries on the nanomachines will run out soon. I guess we won’t meet again.
Honestly, it would’ve been far more interesting if the plot involved addictive combat drugs instead of nanomachines. You could have PMC’s literally fighting each other for the chemicals. Then Liquid Ocelot has the ultimate combat drug, which the PMC’s take, but forces the PMC’s to fly under Praying Mantis, or whatever.
-Speaking of MGS4, I hated ID tagged weapons. DREBIN injecting blackmarket nanomachines so they can use weapons seems like an extra step. If he can do that, he can probably remove the ‘ID tag’ system of the guns to begin with, and if you know anything about guns, the idea of ID tag guns being impossible to bypass is laughable.
-Didn’t like the B&B unit. Seemed like a Kojima fetish thing for the sake of it being Kojima fetish. Seemed lukewarm and samey compared to the other mini-bosses of the series.
I was lukewarm with Metal Gear Rising. Didn’t feel like a metal gear game. It’s a good game, I enjoyed playing it.
Metal Gear Solid V feels unfinished because it IS unfinished. Repeating certain missions under higher difficulty to beat the game is not good game development in my opinion. Would be a 10/10 for me if the game was complete. We needed that Eli fight with Sahelanprothus. We also needed a fight against Psycho Mantis to knock him out (bc time paradox obviously).
-Konami’s treatment of Hideo Kojima. Why cook the golden goose, I’ll never know.
These are the least favorite moments I can think of off the top of my head.