Throwing my hat in the ring as pro-alignment system for 3.5e (la la la 4e I can't hear you!)
You need to respect that it's an integral part of the core mechanics of the fantasy setting. Alignment forms one of the basic building blocks for the universe. Every creature in the game has an alignment, and it's an intrinsic part of their character.
Some creatures are simply always a certain alignment, such as extraplanar monsters. Devils are always lawful evil. Demons are always chaotic evil. Angels are always good.
This is a content issue, not a mechanics issue. "All angels are always good" is a characteristic of the setting. "All angels always want to further the power of heaven no matter what" can be a characteristic of another setting. Both settings can be played in D&D, even using alignment rules (just give the grimdark setting Angels a different one). You're arguing that the default list of creatures in vanilla D&D (Greyhawk? Forgotten Realms? Ravenloft? Spelljammer? Eberron? Iron Kingdoms?) is neatly categorized in Always Evil/Good/Neutral. Yet, creatures are removed from that list and new ones added all the time. There's an actual description on HOW each creature is Evil, you know. It's not like they give you "Alignment!" and you go "well, these guys are Evil so they must keep slaves and beat them, and kill old ladies for the lulz."
You forget that "good" is always a word even if "Good(tm)" is not an Alignment. "All angels are good" can work without a Mechanic, just by saying it, let me show you: "Angel: note: these guys are really good!". D&D will tell you to guess what it means anyway even if you write it down in a box that says Alignment.
If you have too much of a hard time accepting that alignment in a D&D world is an objective, measurable thing instead of a subjective, indefinable quality, remember that some things in these worlds just simply work different to real life. This is a world of levels, hit points, skill points and attack bonuses. These things don't necessarily have a discrete representation in the game, but they exist and are just as valid as alignment. For better or worse, this fantasy world has a line in the sand where morality exists in nine defined flavors, and your character as well as everyone else will be in one of those nine boxes.
But there's the problem: Good and Evil in D&D is not an objective measurable thing. As in, the behaviors that define them are NOT objective at all (they are Measurable, only because you glow Evil or you glow Good the more evil or good things you do). The game still tells you "well... Good aligned creatures do good deeds... and stuff. Use your common sense, duh!". Or to ask your DM (who then proceeds to tell you that Attacks of Opportunity are always evil because he's a big turd blossom). There's not a cut-and-dried list, a menu a-la-carte where you can verify if any single thing you want to do falls in Good or Evil aligned. There are guidelines, sure: don't steal from people that need it more than you! but it's okay to steal from people that have too much don't like to share (OR IS IT?!)".
The whole point of "what happens if you remove alignment" was to show that it's this: nothing special. Two spells stop working (maybe more), and monsters aren't cookie-cutter anymore. That's it. This is not an argument that "alignment systems are bad and shouldn't exist anywhere ever!" It's simply showing that in D&D specifically, alignments hardly even do anything except so that someone can yell at you "alignment shift!" or as a crutch to avoid writing down on your character "my character is always helpful with children but hates abusive authority, yet will respect a benevolent ruler"
Alignment shifts are also meaningless, they do the following:
1) You decide beforehand which is your alignment so that you know what things you're allowed to do.
2) You do things that aren't part of that alignment.
3) You get told which alignment really corresponds to the things you do and to change it.
So, now your alignment is a different one than the one you thought was your alignment when you first wrote it down...
Then later.
4) Your character decides to do different kinds of things.
5) You get told that your alignment is now different.
6) You get to do the new things that you decided to start doing from now on, because of the new alignment (which you could do anyway! except... that they changed your alignment).
So in the end, the Alignment is a label that tells others, what kind of things you do, but don't prevent you from doing different things, doing them enough just changes your Alignment?
But Alignment matters because of magic. And spells that say "if alignment = +1 then...". Which is a really tiny subset of spells anyway. And that normally don't work on creatures that don't radiate their alignment (Clerics, Paladins, and outsiders/undead). May as well make the spells based on Heaven/Hell allegiance instead of actual Goodness/Badness.
In fact, Clerics don't even radiate their own alignment, they radiate the alignment from the deity that gives them spells (which can be one step apart). And Paladins only ever radiate Good (Heavenly!), because if they become Evil and fall, they don't suddenly radiate Evil -their Heavenly Radiation simply stops, and they have to actively seek a new career (that radiates Helly!).