There are plenty of mods that ad perks, or even redo perk system almost from scratch. Ordinator is probably one of the most popular ones. Odin - Skyrim Magic Overhaul from same author is also currently trending fast.

Kinda like Runesacep though? I don't know any mod that would do exactly that. Number of perks in overhauls are vast though, so you don't end like "all powerful in every aspect" kind of character as easily than with vanilla perk system.

Ordinator I already know about. Beside I love the additions it gives, It still contains the same vanilla perks.
What I seek is a mod that not only add new perks for different skills, but also those perks directly influence your character.

For example, the mining perk. If I level up the mining perk, I can get more ores from mining rocks, aswell as more gems. As an extra effect, that could also make the melee combat of my character stronger, aswell as boost the stamina.

Hmm... I don't know exactly the mod what you are after. However, you can try Disparity and Pumping Iron with similar effect. It does not grant you any perks though.

Disparity from krytpopyr allows player body mass to affect on damage they make in melee.

Pumping Iron from Gopher allows growing body weight with manual work, like fighting, mining etc.

I used that combination with my shaman build. He started as skinny, dirty long bearded forester, who could barely kill a wolf. He grew some body mass later on. The jump from early game "AAAAAAAAA! SKEEVER!" to end game was notable and very rewarding.

In addition, Complete Crating Overhaul Remade from krytopyr has MCM options to give XP from several labors. I used Community Uncapper to slow down the general XP rate, so that those labors didn't end up over leveling my character.

That is all I can come up with right now.

Edit: Fixed some typos. I am still finishing up my morning coffee.

I'll check those out. Thanks.