There are arguements for both sides. Don Wang sort of just said what Tycho said on his Penny Arcade blog (eerily similar language usage too).
My stand is generally this: in a game, an interactive medium, rule of thumb should be that you don't show something that the players themselves would rather be doing. RPGs tend to get away with this, sometimes far too often, but oftentimes 'cause the mechanics don't work that way, and gameplay/storyline are seperated.
Devil May Cry 4 got a lot of flack, however, for having bombastic fight scenes that we watch, and can't really interact with.
This has been combated, in a fashion, with the addition of Quick Time Events, though these, of course, have also been criticized, most prominently by Yahtzee.
Metal Gear Solid, however, has usually played a steady tightrope with these things. The first MGS did this really well, using cutscenes to set up really cool shit that WE, the player, would do. MGS2 and MGS3 included things like Snake doing CQC and all that jazz, and people give it flack in the manner Don Wang described, that the stealth doesn't work for these bits.
I disagree, to a point. You see, if the cutscene abilities were in the game engine, the game would be broken, because there would be no reward for stealthy gameplay. Additionally, most of the cutscenes involve Snake being seen, caught, or attacked by enemy characters--which, in a Metal Gear game, is the worst possible scenario. The idea is stealth, and the actual game engine is built to encourage stealth. Cutscenes, being worst possible scenarios in terms of both the game's narrative and the game's mechanics, require a means to return to the status quo, and this is acquired through fancy acrobatics and all that weird shit that we have come to love about Metal Gear Solid. Its acceptable, to a point, because it's A) entertaining a
a means of circumventing the game engine in order to emphasize a certain point, that point being that Snake is a super-soldier, capable of handling any situation. If you could handle any situation in the actual game mechanics, the game would not BE a stealth game anymore. So, yeah, while it may get irritating to enviously watch Snake take down seven guards, frankly, its better that we at least get to see it and still enjoy a game that isn't broken.
Now, boss fights. Boss fights I actually always liked in the MGS games, excluding MGS2 because most of them were either very cheap or very dull--Fatman being cheap, Vamp being dull. Like the cutscenes, boss fights are sort of the "worst possible scenario" for Snake, as he's been found out, and now must fight to escape/survive. However, these boss fights have never felt overly difficult because of the game's mechanics. Look at the Revolver Ocelot fight in MGS1. In the original, its not too hard, but it can be challenging because it's likely the first time you extensively have to use a pistol, and there's no first person aim. Yet, the game was built without a FPS aim, so the boss battle is still a bit challenging, but easily doable. In the Twin Snakes remake, we have the same boss battle, but its fucking retardedly easy because you can actually follow Ocelot with a gun in FPS mode and BOOM! Headshot.
Every boss battle, though, generally takes advantage of different aspects of the game system, forcing the gamer to "think on their feet", similarly to how Snake would. Stealth may fail at times, and it is at those times that both protagonist and player are tested. Psycho Mantis was a great example of this--for Snake, his mind is being read. For the player, his playstation is screwing up. Sure, there's no stealth, but none of the fights felt UNFAIR because of how the game worked, ESPECIALLY with the addition of FPS aiming in later games.
Metal Gear Solid 3 takes this one step further by giving you larger arenas to fight bosses, and actually--with camo and the like--encouraging you to hide from bosses and ambush them, enabling Guerilla warfare. Examples of this can include the End and the Fury, but the Revolver Ocelot fight and especially the final fight against the Boss also take advantage of the stealth camo mechanic, and thus further integrate game engine with the game's boss fights.
Frankly, there's been really few poor marks to strike against any MGS game's actual gameplay. Even the original, without an FPS aim, is still an amazingly fun game to play, and each later installment just keeps building on to that. In fact, the biggest complaint you can give the series is that, since it is so fun to play, when you are forced to watch the game instead of play it, you get annoyed because you are having so much fun just PLAYING.