Bionic Commando (referring to the 3D romp with Spencer voiced by Mike Patton; vocalist of Faith No More).
I loved this game to pieces. It was brilliant, the bionic arm's physics and mechanics were PERFECT, and really...despite it having a typical action fare plot, it was pretty well told, was a great homage to the original (on NES; continuing plot-line, not a remake), and was pretty relevant to the timeframe it was projected to. This is a game that I honestly felt blew all its shortcomings out of the water. Then possibility ate them and spit them out.
However, it has its glaring flaws:
1) The radiation and water. The former, I actually admired at first because it was such an interesting way to make the game feel like it was an open world despite it being incredibly linear -- it was explained right out that bionics are extremely sensitive to radiation, which I found funny, because it isn't exactly a healthy thing to be in contact with, to begin with. The water, not quite as much. The problems I had with them were pretty simple, though...the radiation boundaries were excessively merciless, 90% of the time. You'd go from getting your low-key rad notification to the "HOLYSHITGETOUTOFHEREBEFOREYOUEXPLODE!!!" buzzing in a gorram heartbeat. If you happened to be airborne, at the time of venturing a little bit off your mark in some areas, you seriously prayed for a miracle, because you were pretty much guaranteed to die.
The water, on the other hand...well, the logic for it seemed reasonable -- your arm is really heavy, and you'll sink. If you're not close enough to something to grapple, you drown. Fair, but seriously...they lay this on you when you approach a stage that is pretty much COMPLETELY IMMERSED IN WATER. It ends up becoming one of those beyond tedious pitfalls that don't really serve to hedge you in, but end up making the claw-swinging feel like a gimmick sometimes, and some of said water levels (of which about 80% of the rest of the game is, for the most part) are beyond frustrating.
2) Checkpoints. For the most part, the checkpoints are actually very well-balanced. They're reasonable, give you a decent challenge the first time playing (and on harder difficulties), and come just in time to repeat the cycle. There's about two or three, though, that just exhibit some sort of really malicious intent from the game's designers. One off the top of my head is in Port Anderson III; you hack a relay, then get confronted by a wide variety of challenging enemies in a damned-near completely submerged area with a couple radiation pockets, then get assaulted in the next stretch by a bunch of grunts with a sniper so far off you can't hit him with any of the weapons given in that section of gameplay, and there's no checkpoint between, where the majority of the game would have easily had a checkpoint between two sections that could so easily kill you. In Commando difficulty, you'll see the former portion because of that sniper in the latter section so much, you're bound to lose hair (or break a controller, if that's you're thing).
3) Commando difficulty; not really in general, just specific portions. One really annoying trend is with the bosses. They're the common Far Too Powerful Boss with One Miniscule Weak Spot variety, and most often, in that specific difficulty setting, pretty much anything they throw at you is a one-hit kill. Sure, I love a good challenge, but when you're being forced to play through the same fight over, and over, and over because you can't swing the camera in time to dodge a second quick attack from the opposite direction, or you eventually eat dirt because they take a good dozen or so hits and everything they dish out will insta-kill you if you're not wholly and completely out of range, it starts becoming a boring routine. I still managed to punch through the game at a decent rate and didn't die a whole lot, but some of the encounters are just a nightmare on the Normal setting, let alone Commando, where a light breeze is likely to kill you (yes, even with all the health upgrades). The funny thing is, the AI isn't improved at all. There's just a drastic increase in the amount of health enemies have, and an even more drastic decrease in the amount of hits you can take.
All that said, the game is wonderful, such a joy to play, and definitely underrated (and since it really didn't do so well, is generally pretty cheap to pick up; I got mine at EB last year for $8), and I just have such a blast playing through it a couple times a year. The story didn't really go stale, for me -- I still knew what was going to happen after the first time through, but it didn't really bother me, nor was it my big focus -- and the gameplay is just so engaging.
Those three things, on the other hand...
Well, two, really, because I'll never touch Commando difficulty again, now that I have the trophy. Hard is a pretty good challenge, itself.