Both Kingdom Hearts' and Metal Gear Solid's second game had vastly more complex plots than the first (and made the series as a whole more convoluted).
Both are named after an object of great power which is constantly being fought over, and usually comes into play at the middle/end of each game.
Both series have a western-style gunman (with a gruff voice) who at first seems to have little bearing on the plot, but later is revealed to be pulling a lot of the strings. He appears in the prequel as his younger self, and fights that game's protagonist.
Both have a brown-haired main protagonist who is clueless about what's happening around him, and is manipulated into doing the bidding of those who want power.
Both introduce a blond-haired prettyboy protagonist in the second game.
Both have a prequel starring the primary antagonist of the series, who turns from good to evil in a dark sequence of events.
Both (will) have a final game which wraps up the series and explains any plot holes of the previous games.
Both are named after an object of great power which is constantly being fought over, and usually comes into play at the middle/end of each game.
Both series have a western-style gunman (with a gruff voice) who at first seems to have little bearing on the plot, but later is revealed to be pulling a lot of the strings. He appears in the prequel as his younger self, and fights that game's protagonist.
Both have a brown-haired main protagonist who is clueless about what's happening around him, and is manipulated into doing the bidding of those who want power.
Both introduce a blond-haired prettyboy protagonist in the second game.
Both have a prequel starring the primary antagonist of the series, who turns from good to evil in a dark sequence of events.
Both (will) have a final game which wraps up the series and explains any plot holes of the previous games.