You still haven't answered the question. How do you propose team dynamics could work? Remember, in Skyrim and TES in general its is very easily possible to be good at multiple things. TES is not Final Fantasy Tactics or Final Fantasy XI where your "sub job" strength was cut in half, in TES and Skyrim I can be both a very powerful Destruction Mage and a very powerful Warrior, especially if I have any sort of ability to abuse/exploit or even have just have access to a decent crafting system.
First, let's all agree that a skill based system is
essentially a class based system as every skill combo in the end becomes its own class. Now, the scenario you describe is only an imbalance if you define balance as "all 'classes' should be able to take down any other 'class' with equal prowess". Not only is this immersion breaking as hell, but detrimental to the gameplay. Yes, while a jack-of-all-trade "demigod" that your scenario describes is a mighty foe, it's important to note that his power growth is
much slower, so you're only likely to meet him near end game, and every player can only do a finite amount things in a finite time interval regardless of combat system. So, in the end, it doesn't matter how all-round you are, you're still "specializing" in that time interval. In this scenario, team dynamics
shine as you all must contribute in the fight against the "demigod". Pound him with magic and arrows while he's in melee, kite when he's in heavy armor. Support your allies.
Suppose there are then multiple "demigods" teaming up against you. Same strategy essentially applies. In fact, it asymptotically approaches a numbers game as the groups get larger.
The
Uomo universale of MMOs is not the devilspawn you make it out to be.
How are you going to handle the balancing of the PvE, not to mention the PvP, if I can make Destruction, One-Handed and Heavy Armor Major Skills?
PvE: Variety. Against that particular build, quick and ranged creatures can easily outmaneuver you, since your heavy armor weighs you down, and dodge your magic as all attacks take time to "connect", but still leaves them vulnerable to similar builds. Alternatively, NPC with spear, light armor, spell reflection. This counter build, while weak against e.g. arrows or the stray hammer blow to the face when it made a mistake, has good enough range to poke you to death while remaining outside yours and the spell reflection will seriously make you reconsider using magic. Given enough variety, balance is automatically achieved. Hell, a single restoration, illusion, short blade NPC build can kill you. Buff up with reflect spell, paralyze and stab. Just watch out for arrows.
PvP: Pros and cons of skills. Or in other words, variety. Just not predetermined. The beauty of the skill based system is that you have a wider "class" variety. Thus, while every "class" is good against some, bad against others, if you team up to cover your weaknesses, you've achieved "balance". This makes sense, as no one worth his brain would go up against his "anticlass" without preparations. And yes, even the crafting system has its limits on the amount of support it can provide. This isn't Skyrim/Morrowind where you can pause the game and keep chugging potions.
How are you going to handle balancing PvE, not to mention PvP, when a group of those types of builds are formed? If you can handle said super group, you realize that it can completely screw the balance off for those people who spec as more specific classes/archetypes. If every monster is balanced to handle the super group, what the hell kind of chance does a group of strict basic Warrior/Healer/Tank going to have?
Same principles above applies here. And for added suspense, make sure that the "class name" is hidden, if there is one. You'll never know what aces they have up in their sleeves.
Also, how are you going to get these people together? Are you going to have them search for other players based on Major Skills? Minor Skills? How are they going to be able to sift through the players that have One-Handed and Block as Major skills when they are looking for players with One-Handed and Archery as Major Skills? You could have a wickedly cluttered and complicated searching interface. A set class system (with some divergence) is simply easier to handle all around. That's why it's done so often.
I can easily see a tick-box system work, where you chose the preferred levels for preferred skills (and attributes if included). It's easy to use and makes sense. If you apply for a job, don't mention your skills and instead only mention that you're an engineer, then clearly the employer will have trouble determining if you're the person for the job.