You also keep painting a very broad picture of what that "one" problem is without providing real concrete solutions.
Again, I played Mabinogi for years. And that's the only MMO I can think of that comes anywhere close to these ideals you're talking about. But that game was built from the ground up from the very start around: 1. No raiding. 2. No classes. 3. Focus more on character customization and "fantasy life" with combat tossed in. And even that game if you wanted to have access to everything, you still had to do "content you didn't want to do." Didn't like fighting and only wanted life skills? Awesome, fine. But you want to get to new areas or access flying? Too bad, you have to do combat oriented story.
Online games are all about give and take: if there's content you don't want to do, you simply just don't participate in it. Just recognize you're not going to get the perks that come with doing it. You instead focus on what you want to do and work with that instead. Changing combat won't change that fact. No one is holding a gun to anyone's head saying "You have to raid!" No one is saying you have to use DF. If you really hate the negatives of either culture, that's what FCs or friends or both are for. Or again, petition to have NPC dungeon options instead.
Trying to take a game already almost two years old and completely changing it on its head isn't going to happen. Now if you or anyone who agrees with you has concrete examples of the skills you'd like to see or how a skill tree could work with what's already here, then you're more likely to get what you want. But two years in you are not going to get Square to flat out throw away the combat system this game is built upon. Your best bet is something that fixes the parts that are currently broken (certain skills are useless right now. Why is that and how can we fix them?) or does something to enhance our role interchangeability (If you pick to be a DPS tank, you can suddenly use cross class skills from Classes ABC instead of DEF, but not both, as an example).