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.
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? 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?
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.
First of all, I'd like to point out that class systems are
not somehow magically easy to balance. That's why Blizzard is
still making changes on a regular basis. They keep chasing an imaginary unicorn that constantly seems to elude them(because it doesn't exist).
Second of all, This is exactly why I said that a lengthy beta would need to be held. To find the closest thing to balance as is feasible. To see what players try to throw at your world. To find the unexpected synergies. And then to make changes where needed. This is no different than a class based system, abilities are known. It's just how they work together that you figure out.
Now let's take your Heavy Armor/One-Handed(I would go with the more diverse skills of earlier iterations)/Destruction build. Well he can't cast spells and swing his sword at the same time, so this character has two methods of offense and has possibly sacrificed some defense to do so. Possibly weak against illusion(fear, calm and fury effects being particularly bad) and conjuration(giving you other things to worry about), and eternally frustrated against someone that specializes in alteration and restoration(who can magically mitigate and negate damage) Marksman/Illusion could use hit and run tactics against him, ducking behind walls and vanishing only to take a shot and start the whole thing again. Frankly, the only real advantage your combo gives is equal combat viability at any range. Certainly, there will be builds that are more advantageous than others in specific situations, but you might as well complain about Mortal Strike spec'd Arms Warriors being better for PvP than Prot Warriors in Vanilla WoW. The players will sort out what works best,
The important thing is to make certain that every skill is useful. If someone wants to focus on smithing/enchanting/sneak as their majors, let them. They'll be great for crafting and can travel through hostile territory unscathed. So what if they can't fight? They serve the purpose of the player that created the character without making him slug his way through combat so he could make a better gauntlet. You could have speechcraft allow a player to negotiate substantially better quest rewards and use skill specific bardic abilities for social situations. Now a character with speechcraft could be desirable to get a particular item that couldn't be found otherwise, but is also useful for a goof-off character that just wants to hang out in the local tavern and sing. Mercantile would have obvious uses, but could also have perks that benefit a character in player-to-player trading the way finance skills work in Eve.
So, to reiterate:
1. Balance is an illusion that can only be settled on, never actually achieved(without class homogeneity).
2. Classes or skills, there will be cookie cutter builds
3. Skill-based allows for more interesting cookies.
4. Beta will help balance things in relation to the game world.