The way I always imagined this system is similar to how vocations work in LOTRO. While there are no non-combat classes, every player can choose to pick up a vocation. That vocation, for instance the one I usually chose, could be Yeoman. Among others, Yeoman could create light armor, cut wood, and I believe farm, although I'm not 100% on that. In total, there were around 10 skills, light/heavy armor crafting, woodcraft, farming, prospecting, smithing, and several others, and different vocations occasionally would share skills, although they may not have the prerequisite skill or they may be the base skill to the end product.
In this system there was also leveling, but it was not for the entire vocation, rather it was purely for the skill you gained exp in. For instance, if you mined an ore, you would only gain exp towards the prospecting skill, not towards your entire vocation. This encouraged more rounded game-play, making players use all 3 of their skills as opposed to using one skill they found easy to use and benefiting in every other skill.
In this way, the warrior/crafter specialization system could be modified to fit a system like this; where you can level up your woodcutting and tool making, but not while you leveled your mining. This way, you make sure players have to do a bit of everything in order to become a true 'master.' In short, it's like a system of sub-skills that you must master before you can master the main skill, which I think would be very neat.
I also really like the system proposed at the start of this thread.