The changes to the game, are in Blizzard's opinion the best way for the game to move both to keep existing players (a balance between challenge and content everyone can do/see) and to attract new players to the game.

Basically nothing has been designed from the point of view of helping or hindering multiboxers. Sure, as long as we stick within the ToS/EULA, we generate more revenue than if we were single boxers. But even if you were to count every person who had two accounts (even those who never log them in at once, or perhaps use the Alt-Tab method for trading between accounts) as a boxer, boxers are a very small percentage of the player base.

Click to Move has been an option in the game for a very long time. Interact With Target was brought in to help people with disabilities have an easier time with the game. Sure, those two have combined, to really open melee teams to boxers, but neither option was put in specifically for boxing.

Click Castsequences required initial configuration, and their removal follows a trend. With Burning Crusade, Blizzard broke the ability for me to macro a finishing move if I had 5 combo points, but to cast a combo point building move with 4 or fewer combo points. They have removed the ability for Decursive to automatically target someone in your raid, choose the correct decurse, and decurse that character while you play your Paladin via auto-follow and button mashing with your monitor off. A click castsequence is mindless play, where once the macro has been configured, you make no choices at all, just mindlessly mash a button; as a ranged DPS you could auto follow a friend and one button mash most of a raid. Removal of mindless actions or addons/macros making choices for us, is not aimed at making boxing hard but rather towards making the game more challenging.

Proc based abilities were put in, to keep combat as a dynamic activity. Looking from the perspective of a one-boxer... you are a tank, DPS, or healer, you receive a proc which occurs at random intervals. If you notice the proc and click the relevant ability you gain a benefit from doing so. From Blizzard's point of view, these should be impossible to macro precisely, forcing you to react to relatively random events; that gives an edge to perceptive players or those with quicker reflexes, and helps to keep every encounter more exciting then a one button mash technique. Sure as boxers, we can approximate the clicking of procs, but it won't be as effective as one-boxing.

The healing changes are to make mana an important resource, rather than an infinitely supplied resource and thus not important at all. In the current end game, they could just remove the mana cost entirely and give players an infinite mana supply. It would not impact the game in a large way. I remember raiding in Molten Core, getting low on mana, and having to decide (for the good of the raid) who got to live and who had to die. This model will encourage DPS to not be idiots and have to be bailed out by healers who waste a large amount of mana to keep up a relatively squishy target, when the tank would have lasted 8x as long for the same amount of mana.

Phasing is an incredible tool. We start in an area, do things to change the world, and the world around us changes because of our actions. Sure, they break follow which is a major annoyance for a boxer. However, 99.397% (just picking a large number) of the player base will be running across a phase line manually controlling their toon. Occasionally a one-boxer will auto follow a friend and go to the washroom; and maybe lose follow because of the phase line. It sucks that those break follow, but that is a very minor consideration against having the world change for players based on their actions.

The game changes over time. I don't like every change that has come, nor do I dislike them all. I'm still playing the game, so that says overall I am happy with it. You have a choice whether it is enjoyable or not; who gives a shit if I like the game when you're the one who is spending your money for entertainment? If you find it fun, then it might be worth a few bucks each month, but if you don't enjoy it, what is the point? Breaks can be healthy and they can renew the fun of the game too, that's another option.