I want to be a sweet ass wizard or warrior that blows stuff up, perhaps has a past that I don't know about yet. Older role playing games you learn about the character, the character does not learn about you.
You are right about the natural progression of MMO gameplay focusing on your character rather than the story, but it doesn't help your argument that MMORPGs have deviated from any point that they were at originally.
MMORPGs have never focused on story progression as a key point of design. It has always been about building your own character up in the world because that is your anchor to the entire universe. You aren't playing a flagship character who is integral to the story's elements but rather someone who has a front row seating to what is happening. FFXIV does a bit to combat this, but in the end, you're just a drop in the puddle of an ocean of Heroes of Light -- and you are almost never the focus of the plot elements moving forward. In WoW, especially the latest expansion, you follow a literal Scooby Doo posse-sized clique consisting of Thrall and Khadgar around the new continent while they do anything that is important for the story. You're a set piece. You aren't important to the story because you aren't part of it, you're just a vessel.
Character progression becomes about numbers, rather than lessons/story/abilities
Story starts to feel more like an option feature, rather than a crucial part of the game.
A long echoed criticism of RPGs (especially JRPGs) since the early days of PS1 games was that RPGs were always about numbers and the story only served to toss you from set piece to set piece while increasing those numbers. Can't kill a boss in FF7? Raise your numbers some more. After you've sufficiently raised enough numbers to do more numbers to the boss before he can make you deplete your numbers, you move to the next set piece.
Incentives to kill, but not to save. Whether this be in PvP or PvE, there are no repercussions to your actions, so it's just mindless killing.
There are games out there that require you to interact with a unit to "save" them. Other games, you kill or disable (XIV calls it a knockout) characters in story quests in order to save someone else. Does this really change how you feel about the whole ordeal?
Companies shame the trinity system, instead of improving upon it. RPG is role playing game, what is the trinity system? Assigning players roles. THIS IS WHY IT'S SO HARD TO GET RID OF, so instead of creating your own horrible system, improve upon the one that's given to you. Make the roles more diverse or make AI more intelligent so players can feel unique and different in their roles.
I think you can easily look at Guild Wars 2 to point at a game who tried to challenge the trinity, instead created its own hamfisted archetypes and did the experience improve? Of course not. It's a lot easier to say "just make it more fun and unique!" but I notice you have omitted any actual ideas on how to do that. I would suggest FFX-2 and the FFXIII series (which I consider to be terrible) to look at a game which tries to challenge it, actually does kind of a decent job, but the experience ultimately suffers because it wasn't enough to save the combat. That being said, how could it work in an MMO? Especially since the MMO audience has progressed to a point that there are hundreds of people eager to do the math as soon as something drops so you can look at something more optimally.