One of the big selling point of a lot of upcoming MMOs (and most past MMOs) is that you can play your character your way. Look at Guild Wars (1 and 2!), The Secret World, The Matrix Online, Champions, etc., etc. Even games with fairly strict character progression and talenting structure, like Star Wars, insist you can play it your way. But, I'm curious what you would need to do, from a design stand point, to really let players play it their way.
First, boss encounters would, almost by definition, need to change because you can no longer guarantee that a single tank-like character is present. I consider this a good change; you will now have to do what D&D 4th Edition did by having varied encounters with various states and triggers to exploit, along with a variety of enemy types. That's emerged in Guild Wars and the Secret World.
Second, you have to find new ways to let people stand out. The Secret World is doing this by making player avatars unique, while Guild Wars is focusing more on personal stories. Not only that, but you put the onus on the player to come up with how they fit into a team. In Guild Wars, I am probably playing something of a classic debuffer; if I play The Secret World, I'll probably play a healer/buffer.
I am still fitting into the trinity, but I have more freedom than selecting a character class. Roles in 4E are a perfect example of this. I can pick a variety of flavors of striker, but they are all striker. The problem quickly comes when you start running into suboptimal things. I'm playing a Seeker in a 4E campaign. Believe me, the control options are limited.
That's the same thing that happens in most MMOs that give you freedom. You can play a handgun master splashing a coding simulacra in The Matrix Online. But, it is so suboptimal that you can't and be effective. Your design forks at this point. You can make the content tiered, with relatively easy content to start (like Diablo III's normal campaign), that steps up in difficulty, expecting people to cull their builds to be more and more specialized and useful as they go up the content tiers. This is the approach Guild Wars 1 took as well.
Your eight random skill Mo/E build probably got you through most of Ascalon and Kryta just fine. But, once you started your way through the jungle and the desert, you started noticing gaps in your skills. Content was requiring more from you. You started realizing that some skills aren't really viable, but what was worse, some entire play styles were sub par. You forget all the fun you had with Healing Breeze/enchantment synergies because the "real" content doesn't want you to do that. What's worse, if the game is not as forgiving and open to experimentation (like, say, Anarchy Online or a 4E character without access to extensive retraining), you may cripple your character at an early level and be completely unaware of this till mid to late content tiers.
The second approach is to be unforgiving from the start and demanding of your players. This... does not go over well. Players say that they want difficult content. But the reviews games with actual difficult content gets says otherwise. What you need is the appearance of challenge while still being well within the stress point of the average gamer.
This is not a condemnation of "Casuals are ruining gaming," it is basic puzzle design philosophy. You are not in competition with the people trying to solve your puzzles, er, most of the time. Rather, your goal is to give them the hints they need to overcome the challenge. It is basic etiquette to not cheat those playing with you; finding that balance is more difficult as you have more players.
The game is not fun when you stomp new players into the ground. You make allowances; you explain that that is a bad play, so on, so forth. Now, imagine a game where there are millions of players, and only maybe 250,000, if that, are dedicated enough to learn their rotations, learn what triggers they can exploit, etc., etc. This brings you back to the tiered approach to your content, but then you hit the same problem. Hard mode in Guild Wars is not hard for lots of players, and Normal mode is derisively referred to as Easy mode, or worse.
So, the more you let people play their way, the more allowances you need to give players to play sub optimally. The more you do that, though, the more you space out content and make your old content pointless. The Secret World is trying to get around this by letting you constantly upgrade your skills and learn new abilities from their wheel in a pseudo-level-less system. At the table, you do this by not punishing the new player on every turn, but just once or twice to demonstrate why a move was bad.
The problem is, for MMO designers, they have only a few months (if that!) to impress you. So, the best you can get is a little give and take. You get some freedom in character generation and archetypes, but you don't have complete control. You still need to find and fit a niche, else you run into the Champions problem of ultra durable DPS'ers running about.*
I don't know what the answer is, and I think it is laudable to let people play the way that they want. But, to do that, you have to give your players freedom, painful freedom. Let them recover from it; in Guild Wars and The Secret World you can swap weapons easy enough, in the Matrix everything was based on money so you could, in theory, grind out some cash and slowly start repairing your build. Which is part of playing your own way; you can stubbornly plug away with a melee E/Mo, but your life will be easier if you optimize.
* Tanky DPS is the stock go to for most people in a totally free system. As a designer, you find
it very hard to challenge this archetype. Tanky DPS suffers from not being
as bursty, so if you make things have more health, healers and
nukers suffer. Tanky DPS suffers from not having as good mitigation as a
tank, so any damage you can target at them will devastate non-Tanky DPS
characters. Tanky DPS tends to be melee, so the harder you punish
melee, the more you hurt off-tanks and positional DPS (like Rogues).
Which brings you back to your design tiers, "Let's just make it so being
you can't do this till late tiers, where we can
challenge players and purer archetypes have resources to respond
properly." That's probably the cleanest answer, but again, means they aren't playing what they want.