First of all, this is a new account, but I am a long time reader & play Rufus myself quite a while.
Second, the Akuma Matchup gives me trouble, too, it can be really frustrating to play good Akumas.
But your gameplay has some basic flaws, you should be working on.
I think U1 is the better Ultra on nearly all of the matchups.
Like you’ve already said… u jump to much.
J.HK is quite a good move, but u use it WAY to much. Its quite easy to predict your next move. Also J.HK just isn’t a good move, if your oppenent isn’t jumping. (It’s okay, if you do it late, so it will hit standing opponents.) But still, just go easy on the J.HKs.
Use J.HP to hit standing opponents after your jump-in. Its a good move. It has a nice hitbox and has good dmg/stun. When your opponent is anti-airing and you trade, the trade will be in your favor most of the time.
Use your dive kick more often, too. Its Rufus main tool to get in. You can also use it low to the ground, so its quite hard to aa.
When playing fireball characters… dont always jump-in. Neutral Jump some of their fireballs. Bait them into srk or something and try to punish them.
Try MP-Snake Strike to go over fireballs, while building meter at a safe distance ( dont do this to often, or you will be punished ).
Try to get in, without jumping… down-forward-MK for instance.
Try to go over fireballs with Messiah Kicks from half-screen.
When you finally get a Jump-in, do your BNB ( Dive Kick -> close.lk ( -> close.lk ) -> close.HP -> HP Galactic Tornado ) <- LEARN THE BNB ! ( I know its hard, but its an awesome combo, once you can do it consistantly )
Or when you get an hit of your Jump-in J.HP go into close.HP -> HP GT … or TC into U1. (TC whiffs on Ryu, so be careful)
EDIT: Also, on Akumas air-fireballs… try to get in with down-forward-mk ( roll under the fireball to get in ) or try to trade with your crouching.HP.
Hope that helps,