Hey this is my first guide so bear with me but I've been playing Akali for the past 3 days pretty solidly and dominating 3v3 and 5v5 alike i haven't gone with your typical akali build i know alot of people use gunblade with her but its not really my style so here's what I've got.
I also apologize for lack of grammar or any spelling mistakes.

For runes I just go magic pen marks to cover natural magic resist from champs (additionally if you think you don't need the magic resist or the tenacity you can switch out mercury's treads for sorcerer's shoes) then for everything except quints I get ability power per level because it makes you more powerful late game and 9 times out of 10 you will get to level 18 in a match so getting the most ability power out of your runes and stacking it with Rabadons Deathcap gives you a significant boost. then finally going flat ability power quints for the necessary 20 bonus ability power at the start of the game to obtain Twin Disciplines bonus magic damage buff.

For Masteries i basically put points into anything magic penetration or ability power related along with reducing flash's cooldown some extra attack speed for the on hit effects in the item build and movement speed because i believe mobility is important with Akali.

Okay some people might not agree with how I've done this but I made up this build straight off the bat when I started playing Akali and it is working terrifically for me. I start of with a long sword for obvious reasons to get the other Twin Disciplines buff at the start of the game then follow on to boots of speed moving on to Mercury's Treads or Sorcerer's Shoes depending on opponents after that I go straight for Sheen and yes i know the bonus mana is wasted but the early damage you can pull off by combining the bonus damage from an enemy that has been hit by mark of the assassin and the 100% bonus physical damage after using a skill makes you a formidable opponent early game. After that move on to Guinsoo's Rageblade followed by Phage and then finishing off Trinity Force by this point you will be extremely mobile and a high damage dealer. So to finish off the build then get Rabadon's Deathcap for the large boost in damage to all your skills then Bloodthirster and Will of the Ancients for staying power and survivability this will enable you to stick to your target focusing them down with a lot of burst damage and come out of it with it reasonable amount of hp and pull of double kills and so forth.

I max Mark of the Assassin first because once you get sheen early game it will be your biggest damage dealer and a good ranged way to hassle. taking a point in Crescent Slash at level 2 for a follow up attack to Mark of the Assassin and maxing that second then taking a point in Twilight Shroud early and leaving it there and maxing it last because it is a utility and doesn't become much more useful the more you level it up and obviously like all other champs your ultimate gets maxed at the usual levels.