After reading the OP comment, I decided to tone down all the numbers.
Passive, the new passive is a much more consistent way to take reduced damage. It'll improve the way he jungles, since the damage reduction is quite high after taking multiple successive hits, but won't last long enough to protect him from periodic harass. I reduced the stacks to 3. 60 damage at level 18 is basically nothing before armor. By then, the carries will have an IE or BoTR. when 600+ damage crits are hitting you, it'll reduce the damage, but is still not much compared to 100 armor.
His Q has been reworked into a short ranged dash, stunning the main target and dealing damage to those around the target. It serves the same purpose as his old Q, just more effective at initiating now. Note the range on the dash is only 500, meaning every carry still outranges it (aside from urgot).
His W rework is quite different. I had originally planned it to be for magic damage only, but that would just make him an anti-mage mid. It then had a ridiculous amount of damage reduction and burst damage. Now it deals magic damage so you can't really have penetration on it. It still has a decent amount of scaling, so it won't be too bad. Also, Sion has to make a choice to either continue having 20% damage reduction or a burst in damage. The skill is also completely ineffective when chasing. He has a lower range on his W, so you can't harass with it (especially with the mana cost).
His E will always have less damage until you obtain 1750 BONUS health, albeit his health gain is higher. I don't see how his E will be much stronger until later in the game. His E is not an Atma's, it scales off BONUS health, meaning a warmog will give him 20 damage, but his base health (which I nerfed in lieu of the new health gain) will give him 0 attack damage. There is also a much higher cost on his E, so you actually have to choose when to use it, instead of the current situation, where Sion keeps it on 100% of the time. Also, the increase in scaling will help him gain more HP later in the game. (Higher ELO's, less champ kills more minions) (Lower ELO, more champ kills, less minions). Sion now lacks a ranged attack and shield, making him more susceptible to harass.
His R works like the old one, except it gives less attack speed, and has 60% of the duration. The magic damage seems like nasus's or amumu's, but in reality, it deals a percentage of CURRENT health, meaning it'll continually deal less. At max rank, if you stood right next to Sion for the full duration, you'll have 69.577614% of you health if you had no magic resist. With the standard 30 mr, you'd lose about 20% (compared to Nasus's 60% and Amumu's 32% + 288). The spell vamp helps him heal from his Q, W, and his active R.
Changed the R again. Now it steals speed. This is to alleviate his kiting problems.