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.
YMMV: Bionic Commando
Anticlimax Boss: In most of the original games, the bosses are poorly-designed—it's a bad sign when the typical end boss is a wall that you just shoot over and over. In the new console sequel, the bosses are much easier than the rest of the game—even the final boss and the ending sequences. However, in Rearmed, the bosses are just right.
Often, it was easiest in the NES version to just run around the boss and blow up the reactor with a few rockets without killing the boss.
At the end of the arcade game, after spending a billion quarters fighting your way through the horrible Fake Difficulty, you reach the enemy general... an old man who doesn't fight back, and dies in a couple shots.
Preparations. Specifically, 1:12-1:47. When you go to face Super Joe, that part repeats as you make your way to him, as he engages you in mocking conversation. It's one epic build-up.
Goddamn Bats: A variety across all the games, from the remote-control aces of the NES game to the knife-wielding psychos in Rearmed to the pesky snipers of the sequel.
Demonic Spiders: In the sequel, you will rapidly come to hate the upper-tier Biomechs.
Harsher in Hindsight: Of all things, the Worlds of Power novelization has an instance of this. Early in the book, Rad Spencer has trouble working the bionic arm, but pulls through. When he gets through the area he speaks to the arm, telling it he'll take care of it, and it'll take care of him. Fast forward to the 2009 sequel, where Spencer's arm is his wife...
Jump the Shark: the rest of the sequel's story line suffers from this after Spencer gives the Carrion Device to Super Joe, though certain sequences during that last hour are still very cool.
More Popular Spin Off: To an extent. The Rearmed remake was meant to promote the sequel, but Rearmed is often considered the better game, to the point of getting its own sequel(By a dev made from the remnants of the Rearmed team after GRIN went kaput) in the same style.
Older Than They Think: Most people believe that the NES game came first, but it is a sequel to an arcade game by the same name. Yes, the first [arcade], second [Nintendo], third [Game Boy] and fifth [ PS3/X360 ] games are all named Bionic Commando. Only Elite Forces and Rearmed break the pattern.
Scrappy Weapon: The machine gun from the NES version. It only shoots bullets, and they have a pretty short range. Your regular weapon, that you start the game with, is better in almost every way - it has long range, and with a "turbo" button-equipped controller (or Turbo feature in an emulator) fires just as fast. The fact that the machine gun is kind of out of the way, and a little tricky to actually get if you don't know how, makes it even worse.
That One Level: Area 6, easily. Introduces bouncing mines and a Mook who spawns helicoptering mines in the first area, has some of the hardest climbing and swinging in the game at the beginning of the second area, and then a really tough and annoying rolling mine segment where Giant Mooks throw mines which roll down horizontal shafts, which you can't jump over - you need to use the arm to hoist yourself up (which takes time) or use springboards to go over them. Yeah, this level is hard, what gave you that impression?
This level was actually made easier in Rearmed, with the mines being replaced by non-damaging barrels.
Player Punch: Haley is killed off rather anticlimactically just before the final boss fight of Rearmed. Just in case you didn't already know Hitler "The Leader" was evil. Repeated with Maggie in an even less climactic fashion.
They Just Didn't Care: The sequel's PC port. Every message about what buttons to press are in the form of console commands. Does your keyboard have Left Bumper or Yellow-Y?
Tear Jerker: The ending of the NES version, with Joe's signature.
Joe: I hope this story will be told for a long time...