So I've been having success with B1U2, D2, B3, Ji3, 32 xx Trait so far. Seems like anything that is safe with B1U2, D2, 32 xx Trait is just as safe with the B3 combo.
Some other things I've found that counter it. Note that these CPUs were set to roll+wakeup:
Batgirl's Smoke Bomb
Harley's Line of Fire
Joker's BANG!
Killer Frost's Iceberg, Endless Whiteout (super), AND Black Ice (seriously, fork this vitch)
Sinestro's Fear Blast and Final Shackles
Aquaman's From the Deep and Trident Toss
It seems like most target projectiles (the ones that just show up on you with no travel time) can hit DS before he recovers if the opponent is smart enough to roll+wakeup. If they don't roll, you're pretty safe.
What saddens me though is that Aquaman's Trident TOSS can hit him. That's a little discouraging if you ask me. That projectile isn't even that fast.
So I conjured up this combo: B1U2, F3, D2 xx Trait
This combo covers the weaknesses of the other combo. How you ask? The first combo you listed seems to be beaten out by roll+wakeup projectiles. However, since it knocks opponents far away, they really can't wake up with a melee special and hit Deathstroke. Flash's Flying Uppercut and Lex Luthor's Corps Charge will miss. So if your opponent is touchy with their invincible melee wakeups, go with that.
However, if they catch on and realize that roll+projectile wakeup is the way to go, you can use the other combo I gave you. This combo doesn't push them as far away, and it can be beat by very fast wakeups (like Lex's Corps Charge), but no projectile I have tested seemed to be able to beat it.
Overall, this is still pretty reliable since not everyone has the mindset to roll+wakeup against DS, and we have 2 options depending on how they wake up.