I haven't paid attention to how perks and the like will function in Skywind, but I've had the thought of how I would go about this for a while.
This is something I'd like to make once I've learned how to properly make scripts for Skyrim, it's somewhat of a fusion between their skill systems.
Here it goes:
Pole Weapon skill tree added under the Warrior
Throwing Weapon skill tree added under the Thief
Mysticism skill tree added under the Mage (With things like Clarvoiance, and Soul Gem related spells being moved from their current Skyrim trees to it)
Since there are no standing stones in Morrowind, their effects would get rolled into a birth sign system like the original Morrowind, as new effects for the birth signs. Warrior, Thief, and Mage stone effects would be toned down to only be about 5% skill leveling bonuses.
Classes would come as experience bonuses:
Major skills level 20% faster
Minor skills level 10% faster
This would also apply to custom classes.
Changes to what skill trees constitute which classes would be made as needed given the differences in skill categories between Morrowind and Skyrim.
What do you guys think?

Currently not possible to add new actor values. (Skills) They're all hard-coded.
Throwing weapons have always bean under the Marksman skill (Archery), and I'm pretty sure that poles and spears would be under the 2-handed skill tree.
As for Mysticism, all of the spells could be relocated to other trees.
Though I do like the idea, and think it could be a nice optional mod.
@Thermocrius: Is it? I swear I've seen mods that do it before.
Though looking at it now it seems most of those simply place a second tree within an existing tree.
If that's the case then Spears and Halberd can simply be rolled into Two-Handed, Throwning Weapons into Bows (name could be changed to Masksman or Ranged Weapons or something since Crossbows are in there too), And Mysticism stuff could stay as is.
@Zebulon: Spears and Halberds were their own skill line in Morrowind.
http://www.uesp.net/wiki/Morrowind:Spear
I'm not thermador...
Fixed. Sorry about that, was trying to type fast and my brain put all the wrong things in all the wrong places, and you both start with 'therm'.