Hi, I'm finishing and revising my text yet, I'll publish it all soon!
English is not my main language, so if there are mistakes, please tell me! ^_^

Pros

- Fast and effective jungler
- Does great damage for a tank
- Iniciator
- Ult great for TF and supression
- Great diver, principally with ult
- Has few counters
- Good duelist, especially on late game
- Great persecutor and escapist
- His annoying slow skill can help fleeing allies


Cons

- Completely harmless outside melee range
- Low damage off the jungle on early game
- One of the worst laners in game
- Ult can be easily supresssed
- His performance depends too much of the team synergy
- Counters few enemies

Viable Options

Smite Basic for a jungler and completely indispensable and untradeble.

Flash Best one for skarner, to me. You can use it to jump through walls, to evade a killing blow or (my favorite) to get to your retracted target (ADC usually) to use your ultimate on a TF.

Ghost Viable option for obvius reasons, but it does not gives you the chance that simply pop up near your target, you're gonna have to run for it and take the risk of being slowed/stuned.

Ignite It could be useful to finish a target, but it costs a escape resource. Not the best idea, but viable.

Don't take those

Exhaust You already have one of the best slows in the game and a stalker blade, you don't need that for slow. The AS reduction could be very useful in a duel, but it's not worth the sacrifice.

Teleport It's only really usefful on late game and it costs a flash or ghost. Junglers don't take this.

Heal It could be usefful, but leave it to the support, the other options are long way better.

Clarity You're a mana hungry and this can tempt you. Don't fall for this, it's not worth it.

Do I really need to talk about the other ones? ^_^

The main function of the runes is to help your early game. So, this is what I considered and tested here:

Greater Seal of Armor Helps you to clean the jungle with your life up. Also, your Stalker's Blade - Juggernaut gives you life, but not armor, so this helps you on early ganks too.

Greater Mark of Attack Speed AS is essential for skarner, since Shattered Earth reduces his cooldown with autoattacks. At the beginning your AS is low and you don't have items that gives you CDR yet.

Greater Glyph of Cooldown Reduction Your build gives you 20% of CDR, and it will come only on mid/late game. This 5% helps you a little!

Greater Quintessence of Ability Power + Greater Glyph of Ability Power This inicial AP enhances little your damage with q, but gives a considerable boost on your shield, since you will upgrade it second.