The Class versus Skills is an age-old debate (and by age-old, I mean appeared a few years ago on the internet), and I won't bore you with details of my opinion. I'm pro-skills, for the most part.
The main problem which I wish to address regarding regular skill-based games is the possibility to build a successful Jack-of-all-trades. Your practice of swordsmanship does not deter your ability to fling spells at the enemy, summon demons or sew your own shirts and pants. While it is admirable that developpers wish to ultimately give the players the freedom to build their own class, such freedom should not, in my opinion, be complete.
What I envision is a game that is strictly skill-based, but with skills being linked to similar skills. For example, the Slashing skill, allowing you to use weapons which deal slashing damage efficiently, would be linked to the Blunt, Piercing, Blocking and perhaps Woodcrafting skills. What this means is that someone who is proficient in using slashing weapons would have an easier time picking up the basics of blunt and piercing weapons, doesn't have a hard time learning how to use a shield, and learn to craft things out of wood more easilly. You could always pick up skills that have no link to skills you already have, but such skills would be much harder to learn (skill level increasing slower).
In this regard, a class would be a template for a pre-defined role; a suggestion of a build, no more. Players would be able to create their own character from scratch, picking a few (say, 3) primary skills that start at a decent amount, and a bunch (say, 6) of secondary skills that they start with only basic knowledge in. They would be free to pick skills that are far-away in the skill maze (TM), but those skills would level slowly, and wouldn't necessarily work well together; nor would they have many skills that is close to more than one or two of their starting skills that they could start from scratch and not feel like wasting time trying to level.
I feel my post has been less than clear, so let me explain the idea with an example. You have Bob the Paladin, who has the following skills :
Primary : Slashing (weapons), Defence (spells, from physical attacks), Healing (spells)
Secondary : Blunt (weapons), Blocking (shields and weapons), Protection (spells, from magical attacks), Leadership, Smithing (crafting), Mounting (horses, etc)
Those skills are pretty close in the skill maze. Defending with a shield is close to defending with defensive spells, which in turn is close to healing. Leadership would allow the paladin to gap Mounting and Protection. Finally, the use the blunt weapons is similar enough to smithing that Bob can take care of his own armor.
So here you have Bob the Paladin. But you could build your paladin differently. Maybe Alice the Paladin doesn't care much about smithing and blunt weapons, and instead wants to learn to use spears while riding and cast Holy spells. Maybe Charles the Paladin doesn't care much about that fighting thing and instead wants to learn music and animal taming. Each player can play however they want, and form nearly limitless possibilities.
Of course, the truely hardcore gamer could spend twenty hours a day trying to master all skills; for that, there can be other limitations. But those will be for another day.