Irrelevent. The player is almost always the protagonist in every game. The only game that comes to mind that the player isn't is Lucius.
And why are those mechanics the "challenge" from the story's perspective? Because Glados is testing you. She's a robot and her only purpose is to test, test, and test some more.
Again, irrelevant. You're basically saying the game is on rails and it is. That doesn't mean it doesn't have a plot. It means you can't deviate from the plot without breaking the game. You keep going back to this idea that maybe Glados is the protagonist and Chell is the antagonist. Even if that were the case, it doesn't matter. The confrontation will happen and it will play out the same way every time. With every game, there are challenges that hinder your progress in the plot. Portal's may be physics puzzles where Crysis is aliens and dudes with guns. Delete both from their respective games and there is still a plot but a very easy one to finish.
Actually, let me go back to the confrontation in portal. There is actually two ways to finish that part:
1) defeat Glados
2) get poisoned by Glados
In the latter, Glados clearly isn't the protagonist.
Those are really old games that require rebooting the console to get back to the menu.
You seem to be unswayed by my argument, so continuing with it is irrelevant. Allow me one last attempt though, before I stop trying to argue.
If Glados is extracted from the game, and the final room is changed from a boss battle to a massively difficult puzzle what is lost? You still know the goal is to escape the facility, because you've been on that rail the entire time. You still think something is trying to kill you, because of all the messages scrawled in blood. You still have a "win" state, by completing the mechanical challenges presented to you. Glados is a way to personify the challenges, and frame the construction of the facility as deliberate. Its exclusion would hurt the player's immersion into the situation, but that's Valve making a great game and not just a competent physics puzzle.
Remove the aliens and what do you have in Crysis; nothing. The aliens showing up, because we found their dormant ships, is the plot. Every other soldier in the game is there because of the aliens. If you wanted to remove the aliens, you remove the plot and all enemies. It would now be Dear Esther, not Crysis. If you just wanted a modern day shooter, claim the island is sitting atop a large oil reserve, and the enemies (sans aliens) make sense. Shooters like this require some plot, or at least framing device. Portal doesn't. The second you surround a person with walls, offer them a tool, and let them go they'll try to find a way out of those walls. This is why mental institutions have guards, jails have jailers, and so forth. People don't do confinement voluntarily, and that's an instinctual drive rather than story.
I would propose that Portal has so little plot that we perform an exercise. In the first situation, Glados is a murder bot. You are a protagonist, and must escape the facility to survive. There's a clear antagonist, this conclusion is supported by the messages scrawled in blood, and the final level proves out the theory that Glados is murderous. Simple plot, but reasonable given the data. Now turn it upside down. You're a resident of a psychiatric ward. The entire game is your delusion, as you use a modified fork to jimmy open lock after lock, as alarms blare overhead. Those messages from other inmates are what they spout as you walk by their cells. More delusions from the psychotically unbalanced. "Glados" is in fact the facility manager, telling everyone to find you and not hurt you over the intercom. Despite this, you've already stabbed another patient, what you saw as that very first friend cube. The final confrontation sees you facing off against a nurse with a shot of sedative. Being "gassed" is losing consciousness, and returned to the padded cell you've called home ever since you snapped. Beating the boss is in fact escaping the facility, where you're free to go out and murder the people who put you there. In case one, you're the protagonist. In case 2, you're the antagonist. Both stories are easily viable given that the game has very little plot. If both are logical, then what is the truth? The truth is that the plot was a lazy injection of visuals that framed a competent game of mechanical challenge. Portal is not a story game, it's a mechanical puzzler elevated from obscurity by being tight, well paced, and with enough story elements injected for you to make your own assumptions.
What if Portal was 10 rooms shorter? You don't lose anything relevant to the story. Ten less rooms means less time playing the game, but Valve theoretically could have released the game for less cost and still had it be just as awesome.
Now, assuming you're the protagonist or antagonist is crap. You've cited one game in which you're the antagonist, but that's myopic. Any Star Wars game in which you play the Imperials means you're the antagonist, based upon the Star Wars universe lore. Dungeon Keeper seats you in the role of antagonist. Overlord decided to dress you up somewhere between a demon and the black knight. There's a relatively rich history of you being the antagonist intentionally in the past decade. I'll even bang the drum one more time for this game, Spec. Ops: The Line sure as heck didn't have a gun toting American as a protagonist in any sense of the word. Without a clear protagonist you're doing things because the mechanics require it. Without some clear antagonist the actions serve no purpose. That's the underpinning of a plot driven game.
Now, Portal can't really be plot driven, but that doesn't mean it can't have plot or that it fails as a game. Most side scrolling shooter, bullet hells, and the like have no story. Kill everything on screen, don't get hit, done. Master the mechanics, and success will follow. That is an accurate description of Portal. Master the gun, do the puzzles, good to go. Once the challenges are mastered the game is done. Argue all that you want, but be real. You could play user generated puzzles all day, and night to "complete" Portal, but you stopped playing because the mechanical challenges had been well explored by the game. It isn't a credit scroll that finished the game, it was completing the mechanical challenges. Valve just demonstrated how awesome they are by making both end at the same time. Lesser games fail because they can't do that.
