The game is seven years old at this point so those reasons have been stated over and over and over again. The most common (that I agree with are) that the game doesn't take enough time to fully introduce it's mechanics, stealthing through an active battlefield is really cool but that all disappears when Act 3 turns into a tailing mission that is more cutscene then gameplay. I didn't really think the Jeep section in MGS1 or the motorcycle section in MGS3 were very good but the one in MGS4 is worse and longer then both. The cutscenes break up the game far too often and the actual story content is downright insulting at times. Good moments are ruined by awful moments one after another, and the only satisfactory story arc was Otacon's (kind of) and Snakes...until it was ruined after the credits. None of the boss fights save for Laughing Octopus are very fun, cool or innovative and the Beauties are all just the same character. Drebin tells us about them after we beat them which is pretty pointless. Them being called Octopus, Raven, Wolf and Mantis to begin with is emblematic of the game itself - out of ideas and forced to dredge up the old to make new. The handwaving of "everything was nanomachines" has been shit on to death but going back and retroactively explaining things that didn't need to be explained like Vamp is a rather pointless exercise for a series that had mysticism and raising the dead as an accepted thing before. Everything having to do with romance. Everything having to do with Naomi. Sunny. FOXALIVE (ugh.) The Guns of the Patriots scene. Eva's character assassination. Raiden's character assassination. The Patriots being tricked by dumb shit all the time. The ludicrous Ocelot/Liquid plotline. Everything having to do with the Epilogue. There's just so, so much. I don't think they even should have tried setting a game after 2 to begin with, that was the first mistake.
That said there are a lot of good things about the game. Act 1 and 2 are good, the Ray vs Rex and final battles, while being egregious fanservice, are at least executed well. Snake and Otacon's arcs are done well compared to everyone else's. It's technologically and graphically impressive. But people dislike the game for a multitude of reasons.