Unfortunately I cannot simply ignore the errors in your post:
Otacon and his creepy relationship with his step mom. Like seriously, what the fuck was the point of all that?
- Granted. xD
Ocelot having "Liquid's evil arm" grafted onto his body, something which takes over his entire body and even makes him sound exactly like Liquid Snake.
- Ocelot was acting, in order to manipulate Solid Snake. He psychotherapied himself into believing he was Liquid, at least to a degree.
The ending where they reveal the patriots died 100 years ago or whatever? Did they ever even address this or just brush it under the rug with a retcon?
- You're referring to two separate groups - "The Wise Men", who died around 100 years ago, and "The Patriots" (or the La Li Lu Le Lo) who were formed in the 1970s. The Wise Men were the original Philosophers, and held the Philosopher's Legacy. The Patriots were formed originally as a small group: Big Boss, Zero, Donald Anderson, and Dr. Clark.
I did like the ending of MGS4 with Snake and Big Boss, despite it making absolutely no sense at all. The confrontation between the them was probably the only highlight of that entire game, and if the series had more of those moments and less "Liquid's evil arm" and "Big boss is a fraud" type bullshit those games could have been good.
- Are you referring to where Solid Snake goes to Big Boss' grave to commit suicide, only to be met by Big Boss himself after Solid fails to pull the trigger? There really wasn't much of a confrontation there, unless you count a really old man CQC'ing another old man, then giving him a hug.