As you level up your overall level, does that increase anything else other than health/stamina/magicka?

because my armor rating and enchanting has improved as i level up, is this just for leveling up each of these skills seperately or my overall level?

Your armor rating went up because you leveled up your armor skill. Overall level would not directly affect your armor rating.

The leveling system is amazing.

Yes, no xp grinding. I can just play the game as I see fit and let the xp come.

Things like armor rating and weapon damage will go up as you increase your skills in the relevant skills as well as perk them.