These are what we call the 'YMMV items.' Things that some people find in this work. We call them 'your mileage might vary' because not everyone sees these things in the same way. This starts discussions in the trope lists, a thing we don't want. Please use the discussion page if you'd like to discuss any of these items.
Foe Yay: It's not exactly thick with UST, but Specter seems more than just casually interested in Spike.
Goddamned Bats: Monkeys in green pants will not only sense you approaching much more easily than other monkeys, but they fire homing missiles at you. The red-pants monkeys from the first game were like this except they also punched you.
And in the third game, all the monkeys when not stunned have a very high probability of dodging your net to capture them. This can lead to some epic nerd rage.
Porting Disaster: The PSP remake butchers the controls of the original due to lacking a second analog stick, which the game was designed around.
Sidetracked by the Gold Saucer: Mesal Gear Solid is a GIGANTIC minigame with its own story and gameplay. Leaving the main game for hours of sneaking is common.
That One Boss: King Gorilliax. Hey, whichever character's driving the Flying Turtle! Stop flying under the jet exhaust!
That One Level: The final levels in every game are ridiculously long and have annoying platformer elements. Urgh.
The Woobie: Specter in the Playstaion Move reboot. Here, he was a monkey raised by a female scientist who was forced to be launched into space against his owner's wishes. He was later rescued by the descendants of other monkeys launched into space and was made their leader. He is shown to be rather bitter and sad about all of it, in contrast to his previous portrayal.
They Wasted a Perfectly Good Plot: You need to catch monkeys again, for the PS3, with Playstation Move—wasted potential, in the eyes of some. Imagine playing classic-style Ape Escape games with Move, instead of an on rails shooter.