Masterie's are 21/0/9
summoner skills are smite and exhaust. In that order.
While you are jungling, you are moe relaxed, and it's no problem hitting D to activate smite. In a fight situation I find it easier to use F for exhaust, and R is used just once, usually before exhaust so your index finger can just slide down comfortably without messing up hand position.
Masterie's improve exhaust, smite, critcal chance, critical damage, attack speed, any points that you "have" to put in to get to 21 should be put into armor pierce, and cooldown reduction.
CDR is not very important on Master Yi.
The 9 in utility should go to improved hp and mana regen's to support early jungle..
a point into dead hands, 4 points in exp gain (which get's you to level 3 faster allowing you to grab buff's) and of course, help maintain XP with solo lane's.
your 9'th point will go into increased %15 of buff duration. Where blue buff is used to maintain jungle, and redbuff is used for gank's.
Rune's are very important on Yi.
Mark's I go a mixture of critical damage, Apen, AS. All three affect champion killing, AS and APen will affect early jungle.
Seal's are a mix or armor and HP. Giving you that slight bit of survive in early jungle.
Glyph's I have a couple flat CDR, and a couple scaling CDR. Beyond this I'm still experimenting.
I did say CDR is useless on Yi, but I'll explain.
As you level up a single skill, it's cooldown will decrease as you level it.
I do not get Meditate until I am level 13. By doing this I maximize my offensive output, by creating a higher boost sooner, rather than later.
As you roam between jungle camps, your alpha will ALWAYS CD before you reach next camp. And as for wuju, you can either wait a couple second's, or just initiate and it will CD and become active while you are fighting, doesn't make much difference.
By the time you hit level 18 Alpha will be on 9 second cooldown, med on roughly 25, and wuju on 30, highlander on 60.
By using alpha as an initiate to close a gap, you now have to wait a full 9 second's before you give yourself another leap to close a gap. If you rush in with alpha You lose all utility from this skill. By saving alpha for when you need it you will secure the kill, which since your will be on highlander anyway, your CD will reset. If you went full CDR glyph's, you would really only shave a second or two off alpha, which would still not make a difference.
This goes the same for meditate and wuju. With such a long cooldown, saving a few second's will not help you in battle as much as having some MR per level would.
Regarding youmous and SOTD, I would advise against this. Giving yourself all this AS is overkill as you will too easily Cap at 2.5, and the gold spent towards these item's is better spent getting IE sooner. With 5 crit dmg mark's you can land %260 damage per critical. So maximizing this with PD + IE give's you +%50 crit chance and added movespeed to keep that gap closed. Rushing in with highlander and redbuff allow's you to save Alpha to either leap, or dodge a skill. Notice that when you use Alpha, you actually dissappear from the minimap.
My 3 base item's on Yi are PD IE and Stark's. In lategame (after 5 items) Zerker greaves can be traded in for a second PD which will give you almost the same movement speed, but will now give you a slight bit more AS, and an additional %30 crit.
When you land a %260 critical %80 of the time with Apen from stark's, you can devastate a squishy before they have time to react. With such a high damage output you can rely on %20 vamp opposed to armor's and HP allowing you to stay offensive rather than defensive.
The stronger your offense is, the more pressure the enemy has to build defensive, thus ignoring their own offense.