I've had to limit myself to not "grind" (learn) crafting skills too much or too quickly, since I realized early in the game that if I pursued a crafting career and then switched to combat I would be way too overpowered even on Master difficulty, and the game would stop being fun.
It doesn't take any real skills to level up or to make an uber build. The idea that you could in theory learn all skills the game has to offer is good, but the execution is wrong. I don't know if it would work if you were limited to learn one or two crafting skills. Or another idea is that you only had a certain amount of "points" to use. So you could level up one crafting skills to max or two to half or three to 1/3 and so on. You could also make it so time consuming or slow in progression that you couldn't really master more than one crafting skill during a playthrough.
If we talk about "realism", you can argue that a weapons smith wouldn't have the IQ/skill to work something theory-heavy as the chemical compounds in plants and ingredients. And if you've devoted your life to learning chemistry, how do you have the time to be a master enchanter. Or what so many other fantasy worlds employ is that you need to have flair or an active physiological alteration to be able to use or explore advanced magic in combat or science, and in that way forcing the player to decide how they will play their game.
I love that the game world itself is so open, but I think the overall game experience would be radically improved if you in some way have restricted skill progression.