It certainly effected the way that you leveled up but other than that classes weren't essentially all that different from each other.
You could always use different skills than your (primary)/majors/minors and level them up and become completely efficient in them.
Classes always seemed more like they were there to help role players assume the role they wanted. If people really wanted to role play a type of class they stuck to the skills that defined their class and didn't level up the other skills they had and or limited the skill level they got to in other skills.
The way I see it, this really isn't all that different (especially if you're a role player) in that now you don't even choose your majors and minors now you just pick what you want to be good at. If you're a role player then this really isn't a problem because I (I consider myself a role player) stick to the skills of the role that I play (which is always either a mage or a spellsword). I don't need to "pick" a class to roleplay either of those. I make up the rules for my role play and those often include weaknesses and strengths.
My mage is often excellent at most forms of magick and only uses a staff (he can barely handle a sword and can't even pick up a claymore due to it's weight not even just to put it in his inventory). My spellsword often carries a claymore but can't wield it under normal conditions because it is too heavy for him. So he ends up having to use a fortify strength spell to be able to wield it in battle (if he doesn't he can't use it because it's too heavy).
IMO if you're a role player you stick to the role you want no matter if there is a defined class system or not.