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I'm a huge MGS fan but I gotta go with Yakuza on this. MGS has become so convoluted in the story with some parts just plain ridiculous that I no longer find the story to be of any consequence (still awesome gameplay though). Yakuza, however, has had good story in every single installment. I just wish Y5 would get localized here cause I heard 5 has the best story out of the series.
Yakuza. MGS series has good story overall, but the process to reach there can be quite dire with the long cutscenes and very imaginative things. When I play through it, I have to take breaks to digest the information and just have a break from it. For Yakuza, the overall story is not as amazing as MGS', but I always played to look forward to what will happen next. There are many moments when I felt moved from the main story as well as side quests.
I rate MGS 1-4 highly but Peace Walker was average and Rising has a garbage story. Yakuza 1-4 had really good stories but can't comment on the rest as I never played Dead Souls because everyone said it sucked and the rest never made it out of Japan.
I'm going with MGS, but Yakuza 5 could well be much better than MGS V if they make that one with a story on Peace Walker's level.
Most of the time I'm riding bicycles and on a lot of Colombian marching powder and coffee, forgive me if I act like an #%$hole. Or not, IDC.