So I did the marathon on Tuesday night when the DVD came out. I started with X-Men Origins: Wolverine, and went through the entire series from there.
From watching it in the story's chronological order, and thinking about it even more since then (and re-watching the alternate mind wipe scene a few times since), I am even more convinced that the scene should have been kept. Listening to the commentaries, it's also obvious that Hood wanted to keep the scene, and someone else forced his hand (Fox?) Lemme break down why (wall of text ahead, proceed with caution):
-It's more comic accurate Logan lost his memory via experimentation, not via an adamantium bullet.
-It's more tragic I absolutely agree with Gavin Hood on this, that it just showcases a man who has hit rock bottom, and has nothing left to live for. Watching the alternate version of the scene, I feel -SO- much more emotion when Logan is giving his "I'm just the fool who got played" speech, knowing that he is essentially going to kill himself. It is a very powerful moment. Kayla's reaction is also very powerful. Let me explain:
I'm of a slightly different mindset in my theory to Kayla's involvement in everything. Perhaps I am looking -TOO- deeply at things, but when I look at all the details of that scene, I come to a certain conclusion. The relationship between Kayla and Logan was completely legit. They met on natural terms, fell in love, and lived happily together. But obviously, as Stryker said, "You'd think we'd just let you walk away?" That life was monitored. When Stryker began putting his plots in motion, he needed to finally act on his monitoring of Logan's life. He kidnaps Kayla's sister as collateral, confronts Logan, and when Logan rejects him, takes measures to blackmail Kayla into doing what she ends up doing.
The reasons I think this? Watch the scene where Kayla is explaining her "betrayal" to Logan. Stryker tells him "It was never real". Kayla reacts, wanting to object to that statement, and Stryker responds by threatening to kill her (look at how he showcases his gun to her.) That tells me that there was more to all of this, that the relationship was truly real with the way that she tried to defend against such allegations.
That makes the alternate mind wipe scene even more tragic, because her actions have essentially killed the man that she loved, and there is nothing that she can do about it.
-It makes more sense than Logan just walking away Logan doesn't actually return until Creed attacks Kayla. No action was being taken to stop Logan. Stryker was obviously going to just let Logan walk away from all of it. Why? This reasoning makes a lot more sense to get Logan out of the picture for Creed to attack Kayla.
-Better reason for Creed to help out Logan against Deadpool Victor obviously needs Logan to remember him. When Stryker wipes Logan's memory, Victor now feels a sense of betrayal. He doesn't get the adamantium, and he won't be remembered by even his own brother. It makes more sense now that Creed may have more motive to help Logan against Stryker's plots.
-Better explains Sabretooth / Wolverine in X-Men It's been asked why Sabretooth wouldn't recognize Wolverine in X-Men. Well, here is why. It's not so much that he doesn't recognize him (the taking of the dog tags is symbolic of their history), but he knows that Wolverine won't recognize him. It much better explains those actions.
-The adamantium bullet now makes more sense Through watching the scene, you will see that the mind wiping isn't completed. But having begun, it'd make sense that Logan's mind would now be fragile. 2 adamantium bullets piercing his skull would now make a lot more sense to finishing the job than they do now, where it feels very forced, random, and tacky.
-It fits better with Stryker's claims in X2 When Stryker says "As I recall, it was you who volunteered for the procedure", it is in response to Wolverine saying "You took my life!!!" - implying the memory loss. This would have been that "volunteering" Stryker mentioned. Obviously, Logan has already volunteered for Weapon X, but this only expands on the idea that Logan "volunteered".
-Logan feeling like a man with no other options isn't a bad reason Again, I agree with Hood here. I truly can accept the fact that Logan's mindset is "Do with me as you will, I don't care anymore." Logan already did it once, and while he obviously knows how manipulative Stryker is, I think it makes it even more powerful for Stryker to continue the manipulation of Logan. At that point in time, it is very feasible that Logan just truly does not want to remember any of this anymore, and wants a clean start. While he may be getting it through questionable means, it's a "drastic means require drastic measures" type of deal. I am truly okay with this reasoning, and given the events of the film, I believe it is much more powerful and dramatic than simply being shot in the head with a magic bullet.
I really wish this was the official ending of the movie. I really do feel that it makes the movie 1000 times better than it is now. It gives the movie that dark feeling that it was lacking. I know that sounds extreme, but my biggest gripe with the movie always was the adamantium bullet and Logan not losing his memory via the experimentation. With this scene, the movie becomes more of what I was expecting / hoping for knowing that they were making a movie based on Weapon X, and less of the joke that it has become amongst the fanboys.
I feel that it is a shame that TWICE now the X-Men movies have suffered from bad plot points, only to find via special features / deleted scenes that the correct handling of the scene was actually filmed, but they just made a creative choice against it. It is very frustrating.
It is one thing when you delete Storm's tidal wave from X-Men: The Last Stand, Xavier's "escape" in X2, or Rogue asking for a cure in X-Men, but when the actual movie gets something wrong and there is a scene featured on the DVD of them doing it right, it's very frustrating.
And in my mind, both the alternate Rogue ending in X-Men: The Last Stand, and the alternate mind wipe in X-Men Origins: Wolverine, not just doing it right, but doing it absolutely perfectly.
The closest we can ever get to these being done right is to get director's cuts that cut these movies with the proper versions of these scenes, but even then I doubt that makes those events official cannon.