I agree with so many points that you make here. I'm so glad I'm not the only one who had these thoughts. I think the communication issue is one that's popped up time and time again with House, but this had some especially good points to it. I hope you don't mind me sharing my thoughts, too, even though I'm not...really arguing with you. ;) And I think what happened in the finale really brought to light a lot of what was going on with House this season, which I thought was pretty cool.

So, if you don't mind...(It's mostly a copy/paste from my LJ, but it hits on a lot of your points, so I thought I'd...share this instead of trying to reword it all).

House has had two primary goals this season: 1. To avoid and minimize pain as much as possible; 2. Attempt to be less miserable. Both of those goals can be traced back to his confession to "Amber" (who, was his subconscious even then, so it's incredibly appropriate that his subconscious manifested in the form of Amber later, because he was dealing with the same issues--pain and misery) at the end of Season Four.

These motivations have remained consistent throughout the entire season (though, you can make a strong case for this being true for the entire series), but they became glaringly obvious right around The Softer Side, when House tried methadone, an alternative pain management method in order to become pain-free. His goals started to take even more shape during Locked In, when we learned that House tried to see a therapist. Finally, they became complete during the last two episodes, and they manifested fully in a very compelling way. One of House's focuses through the season, what he perceived as a means to an end and, as it turns out, what he's wanted the most, was to return to the person he was and the life he had before the infarction happened. This was the last time that House was at least less miserable than he is now, probably having a decent life, experiencing some happiness. But it was especially golden compared to what he's been living for the past ten or so years--his post-infarction life.

Every one of his efforts have tied in to his two main motivations, and the 'means' of recapturing his pre-infarction life, where he had: no physical pain, was not dependent on or addicted to Vicodin, was more emotionally healthy (there is little proof for that, but looking at House, it's hard to imagine him being worse off than he has been recently, in the last several seasons), and had a close and good romantic partner, with whom he was in a committed and loving relationship. Every one of his efforts to recapture that life, however, have failed. Going through them one by one: The consideration of a step further into new territory with Cuddy after Joy failed, more than once, and for several reasons (House was not willing to take the risk, and later, when he was considering it a little more, wasn't willing to enter into anything more with her when her perceptions of him were not clear or balanced); the attempt to ditch the Vicodin and utilize methadone instead failed, despite the fact that he was pain free, because he was not willing, in his mind, to compromise his skill as a doctor for less physical pain; and his attempt to see a therapist to improve his emotion health failed, though those reasons are less clear. What is clear, however, is that he had broken down the aspects of his better, healthier, and happier pre-infarction life and, one by one, was trying to get those aspects back in order to minimize pain and be less miserable. But he failed.

Finally, in the finale, House has come to hate his life so much, and is so unhappy with it, and is so devastatingly lonely and miserable, that his brain has made a last-ditch effort to make him 'happy'. For a while, where he failed in reality, he succeeded in his mind, in his fabricated form of reality--this alternate reality. In this alternate reality, he possessed all the elements of his pre-infarction life--the tools to be happier. He was not dependent on Vicodin. He had very little to no pain. He was able to communicate better, display a better emotional health. And he was intimate and close to someone he cared about for the first time in more than three years. Which brings me to the House and Cuddy aspect of the season...

This House and Cuddy storyline has never really been about Cuddy. Yes, her character has been tackling issues, and has been given depth and we got to see more of her. However, Cuddy has operated as a representative of a missing element in House's life--the potential security and comfort of a committed romantic partner. In the past I have said that House and Cuddy weren't truly in love with each other, and I think this finale more or less confirmed that; they were in love with what each other represented in their lives, but not with each other, the people, in reality. This was never a storyline based in romance, but in deeper issues that House (since I'm speaking more about House, I'll stick to it) was wrestling with--issues of loss, and misery, and pain. House considered taking it a step further with her, but it came at a time when he was almost desperately clinging to what was important to him--the people that were important to him. Cuddy became, however, a symbol of something House lacked in his post-infarction life, and his brain used her to fill that hole because she was the most present, most logical choice, the only woman currently in his life that he feels even remotely close to. I don't believe it was an issue of wanting Cuddy the person, (just like Cuddy had never really wanted House, the person, but wanted a specific role in her life filled) but he wanted all those pre-infarction elements to be filled, finally, so he could recapture his less miserable and less painful life.

I think that what House needs to do is to come to terms with himself, and accept who he is, because he's been unable to truly do that. About House and Cuddy, I don't believe that, now both characters have a better (well, Cuddy more than House) grasp on reality--or at least what isn't reality--I don't believe that they will or should pursue a relationship, but I'd be thrilled to see them become closer and more supportive after this. But, I have to say that what House went through and what he created for himself and why was the most heartbreaking thing I've ever seen on the show, and it resonated with me in deeply personal ways. (For those of you know me pretty well and have been keeping up with my life for the last so-many months, should be able to figure out why pretty easily.) I had an emotional breakdown for about an hour afterwards, and it hit me hard, personally. But, I'm relieved to see that it tied together House's motivations throughout the whole season, and that the House and Cuddy thing turned out, for House, to be focused very little on Cuddy herself, but much more on what House missed in his life, but did not cheapen the portrayal or minimalize the significance of any character. (Did I mention that the video montage of the 'reveal' was mindblowingly amazing. It really broke my heart, because realizing your brain has created something like that is humiliating and devastating in so many ways. Also, I loved the bookending of the way "Amber" reappeared, a mirror of her first appearance, and the fact that Kutner appeared as well. But that montage was incredibly well done.) So, all in all, a good end to the season, and a good tie-in with the events throughout.

I admit I was going to skip over this because I thought it was going to be a pro-Huddy look at this season. You bring up some interesting points in examining the relationship between House/Stacy and House/Cuddy.

He wants someone in a Cuddy-shaped package, but not Cuddy herself.

True. Too bad he doesn't want someone in a Wilson-shaped package.

Wilson needs to jump him =P

Agreed!