Here's a shorthand of how I would fix MGS4.
>shorter and less cutscenes
Have more gameplay of core stealth and awkward combat. Have the Act 1 be a sandbox, Act 2 a more linear one, Act 3 almost as linear as the original, then Act 4 and 5 be typical gameplay.
>no one-liners or shitty poetry coming out of everyone's mouths
The plot was convoluted as fuck which is understandable since it follows 2 but within that plot the writing is poofy as fuck, it sounds like an 11-year old girl's diary.
>no airplane gluing the acts together
The game jumped from one location to the next and didn't feel tied together. Have Snake go do the first three acts uninterrupted then introduce the airplane on your way to Shadow Moses with the final battle happening on Outer Haven.
>technology and war
Show civilians running for cover and dying, show more uncanny tech cyborgs with artificial wings replacing their arms, something more than nanomachines and robotic limbs.
Have him look anemic and white-haired at the end of the game when he gets more radiation than your nutsack in front of your PC, make him look 60 instead of 70 and get rid of the mustache.
I don't know where to begin on that but the support team from 3 as the founding members of the Patriots was lazy and cynical, and what brought the series into ham and cheese, you can keep them as AI but have more human involvement with it and still have the support team become involved in some way I guess.
>Big Boss, Eva, and Zero
Keep them in but rewrite it.
I don't know but don't have nanomachines be the reason for his superpowers, don't explain that shit ever.
Make them the ace in the hole for each PMC instead of Charlie's Angels for Liquid, don't have them be callbacks to previous bosses and give them variation in personality and backstory.
Attach him to Rat Patrol I guess to have an excuse for him to reoccur as some dealer trusted and approved by the fed.
Have him be on the support team but the plot should be set in motion by Snake, Otacon, and Raiden's good will.
Don't take his aversion the nanomachines as a laugh, make him unseemingly intelligent and wary of technology and centralization but too scared to object it.
Make it harder to win over a side, usually require a side quest to make them amicable towards you.
Give them more characterization and different equipment based on their country. Have each one based their personal equipment and gear based on their country of origin and size. Have a French/Euro one, an American one or two, a Russian one, I don't know about a Chinese one, and Liquid's. Have little PMCs operate with rebels or the big ones.
Have it take place in Yemen which is the biggest shithole in the middle-east and has had non-stop wars so it's fitting.
Snake goes north to the Jawlan Heights to find Naomi or a still-kidnapped Sunny. Act 2 was the best part of the game so there's not much to change unless that turret section bothered you as much as the one in Act 3.
After Snake escapes from Jawlan he ends up in Europe somehow. Keep the tailing but have more guards roaming, no chase setpiece, have a mobile battle against French/Euro PMC through the sewers to the epic cutscene where Liquid enacts GoP.
Sneak around American PMC, include fauna that can kill or befriend you.
Have it take place on Outer Haven but with the ship far more explorable.
Also it's not that important of a feature but remove the gun porn too or easy access to it, it's nice to oggle at that many accurately-modeled guns but it serves no purpose except with fan justifications that it represents the war economy's and all guns are the same. The only thing I feel strongly about is that Snake should've kept the Mk. 23 or used the Mk. 24 instead of the 1911.