To deal with the crouching issue, on most characters (excepting twins, Ibuki, Oro, Remy, maybe one or two others), you can rush up after a knockdown and from point blank, do d.short, d.jab, and if it hits do mk hurricane, then sp DP. Requires practice, but worth it to have something safe and verifiable. You do have to be right on top of them though or the hurricane won’t combo.
Learn how to use the demon flip (dp+k) effectively. Against characters with no good anti-air (twins, Chun) it can be very useful. It can be especially good if you have them in the corner since you can cancel it off all of his decent normals. Also, never ever EVER use far standing mk. Ken and Chun can punish it, even if they get hit while crouching. It is a bad move and you should just avoid using it against anyone.
Learn kara throwing, learn what pokes put you in range for it, it is very important to Akuma’s game. He has arguably the most useful kara-throw in the game. It has good range, but not as good as Elena/Chun, but unlike Chun-Li’s, you don’t have to be outside of a certain range to use it. Also, in the arcade version, f+mp is unthrowable, so if you mess up and they tried to throw/tech throw, they’ll just get hit.
Oh, and find the topic about ragin demon setups, very useful. Akuma is a much bigger threat when he has full meter since he can kill you for doing dumb things. And by dumb things, I mean stuff like jumping in, or trying to reversal after blocking a ground move.