Most of your high moves miss him. Except 6K, so don't hesitate to use it, especially since yoda is pretty slow. =]
All throws and attack throws of any kind will fail. no flapjack, A+K, FC 3B attack throw, etc, it all fails. Your launchers also don't launch as high. Because of this, you're gonna have to use some dumbed down combos.
other stuff that whiffs:
CH 4KK second hit whiffs
second hit of 6B:B whiffs
Combos to use:
33B > 1A
33B6 > GS B
3B > 1A
3[B| > NSS bA (this is harder than it normally would be but works)
66B > agA
WS [B| > NSS A+B
CH WS [B| > NSS A+B > 1A
anything involving otg GS KK will fail, second hit will miss
At the most basic level, your gameplan is to abuse mid attacks that will be hard for him to dodge. beware of his B+K parry though, as it can parry mids, so mix in some lows as well. Yoda is vulnerable to CF because his soul gauge is only 2/3 normal durability.
Defensively, it shouldn't be too hard to deal with him because he has very few lows and the ones he does have are weak. His 6A+K low knocks down but takes a while to come out and he moves forward low to the ground before doing it so you should be able to see it after a while.
He can do force cancels from his air attacks, which allows him to go into more air attacks. However, there's no mixup from this because while he's in the air the only low he has is a retreating low move that won't hit you unless you're running into him. He does have a mid, low attack with 66AA that comes from the air, but you can punish the second hit with WS [B ] on block, and there's no mixup to the string anyway.