I kinda liked the perk system in Skyrim, but I think that certain skills really need to work some other way. Smithing in particular was just grinding. I think that such skills shouldn't be actual 1-100 skills, but instead just perk trees, maybe with a charlevel-dependent unlocking system (you need to have reached a certain level to unlock e.g. steel armour).

I think that it would be good also because you don't need to craft that many weapons and armour parts for yourself. When you get a perk, you improve what you have or create something new and that's it for a few levels, instead of creating hundreds of daggers (which I guess you could still do, for example for trading, but you wouldn't need to).