Hey, to start off: this is my first post on this forum. I am lurking a bit, following the progress that porting Morrowind to Skyrims engine goes through with great interest. Today, I have read that the skill and perk systems are not set in stone yet.
I will not write an essay but come straight to the point. The skill and perk systems in the Elder Scrolls games have some issues, especially since enemies started to scale in strength with character level in Oblivion. Basically, both skill increases as well as most of Skyrim's perks just provide an improvement of the related abilities by some percent points. Especially with scaling enemies, but even without, this is dull- it doesn't alter combat/crafting significantly, offering a relatively repetitive experience. On top of that, many many abilities and spells are downright boring.
Some modders have already touched the issue. One of them stands out: T3ndo and his Perkus Maximus Mod. He has analyzed the shortcomings of the Skyrim perk system and its branches, weaponry, crafting, the magic schools, and spells, and has overhauled them accordingly. He makes many strong points, and his mod improves combat in Skyrim tremendously without altering the general theme or messing with the lore.
The linked Nexus Mod download page includes an explanation of his approach, his design principles, etc.pp.
It's elegant, and especially mage combat struck me as addictive and far more strategic than before.
Thus: I hope you take a look at this mod before dealing with the skill and perk systems.
It adds so much to Skyrim that it would be a pity if others didn't learn from it and just repeat the original developer's mistakes. Moreover, in my opinion, it changed Skyrim towards Morrowind to some extent, since it reintroduced bigger differences between different weapon classes.
That's all from me. Right now, due to obligations, I can't offer help with the project. Maybe later next year, I will try to enter the team.