This is the set up that I use for Kennen, I'm not the best Kennen but I have a good understanding of how to play him.
The rune set up I use for Kennen is for a few different reasons.
Magic pen for obvious reasons.
Armor. The reason why I get some armor runes is because you ARE going to end up auto attacking people early game to get your W on them. When you auto attack you draw minion aggro. Minions are physical damage.
Magic resist. Flat MR against casters mid.. seems like a good idea, no?
Health per lvl. I take some health per level because I've notice in a lot of cases you tend to get extremely low from ignite during team fights or other stuff. Just nice to have the extra hp to give you that chance to live with 1 hp. >_>
Movement speed quints. The reason I use movement speed quints is because I prefer movement speed over more magic pen or ability power, combine this with Kennens E and you can almost always avoid a gank. If you get boots first you will normally have around 375 movement speed at the start of the game which is extremely good against early games.

Cats.

Summoner spells I take flash ignite because it's usual for casters mid + ignite is pretty ****.

Farming is really easy, if you're doing poorly or low on health farm with q so your spellvamp heals you. If you can take the damage from enemy you can use your E to rush through minions and tag everything to farm.

Keep in mind his ult only hits the same target 3 times. So 2 stuns in a 1v1 at mid if you do everything correctly.