I'll talk about Barbarian, because it's the class i play most of the time.
When it comes to Wrath of the Berserker, my suggestion is: reduce cooldown to 60 seconds instead of 120 (this should be done with Earthquake and Call of the Ancients too), and increase duration to 20 seconds. Then redesign Thrive con Chaos to reduce the cooldown 1 second per 25 fury generated, not increase the duration. This way WotB - ToC will be useful, but it wouldn't be overpowered, and the other runes would be more appealing. Arreat's Wail is and will always be useless... Redesign into "while active, Wrath of the Berserker erupts blood, dealing 100% weapon damage per second to nearby enemies" or something like that, to make it useful and fun to use.
Bash - Pulverize is really cool for AoE skill, but the shockwave should deal at least 100% weapon damage.
Cleave - Rupture should be triggered on critical hits, not on kills. That way it would be useful in the endgame.
Frenzy - Triumph should be triggered con critical hits, same reason as Rupture. Vanguard could also increase attack speed by 2% per stack.
Seismic Slam should deal around 300% weapon damage, and have a rune to pull enemies towards you.
Rend - Bloodbath is useless, redesign it to something like "enemies killed with Rend cause a blood eruption dealing 700% weapon damage to nearby enemies".
Whirlwind is pretty much useless with any rune other than Hurricane, so the solution should be making Whirlwind move at normal speed, and make Hurricane boost movement speed by around 10%. This way the other runes would become much more useful.
Leap should have a rune to remove the cooldown but make it cost fury instead.
Ground Stomp should always deal damage, and increase the area to 18 yd (the area is too little without Wrenching Smash).
Reduce Ignore Pain cooldown to 20 seconds, and make Bravado pull enemies instead of knockback.
Increase Ancient Spear damage, and make it always pull multiple enemies without needing Harpoon rune.
Revenge - Grudge should pull enemies, not knockback...
Overpower - Storm of Steel is so cool! But it would be better if it dealt more damage...
It would be interesting to have a rune in Threatening Shout that made enemies bleed, so it would become both a defensive and offensive skill.
Battle Rage - Ferocity is useless... Redesign it to increase critical chance up to 5-6%.
Same with Sword to Ploughshares... Redesign it to give some lifesteal or something useful... Or at least increase the chance to drop a health globe to 10-20% chance.
Nerf Into the Fray to 10 fury instead of 15... 15 fury is just too much...
Bloodshed is nice for AoE, but it needs some buff... At least 30% instead of 20%.
War Cry - Charge! Should also reduce the cooldown to 10 seconds. Make it a really good fury generator, because you're trading off 20% armor or 20% all resistances...
As i said before, Earthquake should have a 60 seconds cooldown, and it would go down to 45 seconds with The Mountain's Call and to 30 seconds with Boon of Bul-Kathos.
As well with Call of the Ancients, reduce the cooldown to 60 seconds and make it last 20, and 30 with Duty to the Clan.
That's pretty much everything. Sorry for the long post...
I think this is a great idea. Though I also think it's a little complex, and it could be simplified and improved in some aspects.
I don't see why the Mystic should be involved in enhancing skills and runes, she should only enchance and improve items, not skills.
My suggestion is to give the player a "Nephalem Power Tree", where he can spend "Nephalem Power" points to improve different skills and runes. In order to get "Nephalem Power" points, the player should first equip items with a "+X to Magic Power" if he's a wizard, "+X to Mighty Power" if he's a barbarian, etc.
For example: a barbarian could spend 3 points improving Frenzy damage, and once he spent 3 points on the skill, he would unlock another level, where he can also improve the different runes, like "increase maniac bonus to 5% per stack", or "increase the chance of triggering Sidearm to 35%", etc.
To be able to do that, the barbarian first needs to have 4 Nephalem Power points. Let's say he equips a weapon with "+2 to Mighty Power", a ring with "+1 to Nephalem Power", and a belt with "+1 to Mighty Power". If he spends all 4 points, and then unequips the belt, he would instantly remove the last point he spent from the Nephalem Power Tree.
Another way to win Nephalem Power points could be by Paragon Levels, let's say you get 1 point every 10 Paragon Levels, so you will have 10 Nephalem Power points at Paragon 100. This would be another motivation for players to level up to Paragon 100.
So, to make it short: I don't think the Mystic should be in charge to improve skills and runes. Instead, we should have a Nephalem Power Tree, where you can spend these points that you can get by item rolls or by Paragon Levels, in order to improve your skills and runes =)
Edit: oh, and I really loved the idea to grant Magic Power, Spiritual Power, Mighty power, Dark Power and Tribal Power as full set bonuses. That way people will start wearing full sets once again, and not only 2-3 pieces (because 2-3 pieces bonuses are even better than 4-5 pieces bonuses...)
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When it comes to Wrath of the Berserker, my suggestion is: reduce cooldown to 60 seconds instead of 120 (this should be done with Earthquake and Call of the Ancients too), and increase duration to 20 seconds. Then redesign Thrive con Chaos to reduce the cooldown 1 second per 25 fury generated, not increase the duration. This way WotB - ToC will be useful, but it wouldn't be overpowered, and the other runes would be more appealing. Arreat's Wail is and will always be useless... Redesign into "while active, Wrath of the Berserker erupts blood, dealing 100% weapon damage per second to nearby enemies" or something like that, to make it useful and fun to use.
Bash - Pulverize is really cool for AoE skill, but the shockwave should deal at least 100% weapon damage.
Cleave - Rupture should be triggered on critical hits, not on kills. That way it would be useful in the endgame.
Frenzy - Triumph should be triggered con critical hits, same reason as Rupture. Vanguard could also increase attack speed by 2% per stack.
Seismic Slam should deal around 300% weapon damage, and have a rune to pull enemies towards you.
Rend - Bloodbath is useless, redesign it to something like "enemies killed with Rend cause a blood eruption dealing 700% weapon damage to nearby enemies".
Whirlwind is pretty much useless with any rune other than Hurricane, so the solution should be making Whirlwind move at normal speed, and make Hurricane boost movement speed by around 10%. This way the other runes would become much more useful.
Leap should have a rune to remove the cooldown but make it cost fury instead.
Ground Stomp should always deal damage, and increase the area to 18 yd (the area is too little without Wrenching Smash).
Reduce Ignore Pain cooldown to 20 seconds, and make Bravado pull enemies instead of knockback.
Increase Ancient Spear damage, and make it always pull multiple enemies without needing Harpoon rune.
Revenge - Grudge should pull enemies, not knockback...
Overpower - Storm of Steel is so cool! But it would be better if it dealt more damage...
It would be interesting to have a rune in Threatening Shout that made enemies bleed, so it would become both a defensive and offensive skill.
Battle Rage - Ferocity is useless... Redesign it to increase critical chance up to 5-6%.
Same with Sword to Ploughshares... Redesign it to give some lifesteal or something useful... Or at least increase the chance to drop a health globe to 10-20% chance.
Nerf Into the Fray to 10 fury instead of 15... 15 fury is just too much...
Bloodshed is nice for AoE, but it needs some buff... At least 30% instead of 20%.
War Cry - Charge! Should also reduce the cooldown to 10 seconds. Make it a really good fury generator, because you're trading off 20% armor or 20% all resistances...
As i said before, Earthquake should have a 60 seconds cooldown, and it would go down to 45 seconds with The Mountain's Call and to 30 seconds with Boon of Bul-Kathos.
As well with Call of the Ancients, reduce the cooldown to 60 seconds and make it last 20, and 30 with Duty to the Clan.
That's pretty much everything. Sorry for the long post...
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I don't see why the Mystic should be involved in enhancing skills and runes, she should only enchance and improve items, not skills.
My suggestion is to give the player a "Nephalem Power Tree", where he can spend "Nephalem Power" points to improve different skills and runes. In order to get "Nephalem Power" points, the player should first equip items with a "+X to Magic Power" if he's a wizard, "+X to Mighty Power" if he's a barbarian, etc.
For example: a barbarian could spend 3 points improving Frenzy damage, and once he spent 3 points on the skill, he would unlock another level, where he can also improve the different runes, like "increase maniac bonus to 5% per stack", or "increase the chance of triggering Sidearm to 35%", etc.
To be able to do that, the barbarian first needs to have 4 Nephalem Power points. Let's say he equips a weapon with "+2 to Mighty Power", a ring with "+1 to Nephalem Power", and a belt with "+1 to Mighty Power". If he spends all 4 points, and then unequips the belt, he would instantly remove the last point he spent from the Nephalem Power Tree.
Another way to win Nephalem Power points could be by Paragon Levels, let's say you get 1 point every 10 Paragon Levels, so you will have 10 Nephalem Power points at Paragon 100. This would be another motivation for players to level up to Paragon 100.
So, to make it short: I don't think the Mystic should be in charge to improve skills and runes. Instead, we should have a Nephalem Power Tree, where you can spend these points that you can get by item rolls or by Paragon Levels, in order to improve your skills and runes =)
Edit: oh, and I really loved the idea to grant Magic Power, Spiritual Power, Mighty power, Dark Power and Tribal Power as full set bonuses. That way people will start wearing full sets once again, and not only 2-3 pieces (because 2-3 pieces bonuses are even better than 4-5 pieces bonuses...)