To me MGS1 is still the best one in the series story wise (MGS3 is close though) : the bosses were all so cool (Psycho Mantis is unbeatable in the coolness category), the story progressed nicely with great plot twists. Even characters you only talk to by codec are interesting (Naomi's backstory is awesome, also she had a slight english accent that I loved but that somehow didn't carry over to MSG4)
MGS4 was also great but the characters were less engaging. I couldn't care less about the story of the B&Bs because I had already killed them when I learned about it.
Also, about Drebin's monkey: the first I encountered Drebin my thoughts during the whole cutscene were "Once this cutscene is over, I'm unloading all my ammo on this stupid monkey" Unfortunately, they don't ever give you the chance to shoot it.
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