Abel's Tornado Throw has two properties, the normal version is unthrowable, and the EX one is unhittable(yet throwable). So its a 50/50 for him everytime he gets into your face. I know that i used Normal Tornado Throw and tossed Zangief out of his Ultra because i know one dude liked to use his SPD. I also EX Tornado Throw Ryu out of his Ultra before too. Shut that crap down lol.

A way to counter is to Jump up really fast (not all the time, else you eat Falling Skies) or backdash. I say backdash because in SFIV, backdashing has invincible frames upon startup. Its little but its enough for you to gtfo. If you're in the corner, then its 50/50 for both of you upon wakeup.

Usually an Uppercut can break those through very well, however if you arent a shoto, and is like say Gen's uppercut, you might have trouble with it. Best to do is to actually know how the opponent plays based on the visual cues and things that they do and try to counter/guess. Against Zangief its alot harder to just jump away in this game...so its about how you perceive the opponent will do.

If its against the CPU just stay the hell back like JKTrix said and keep using long ranged pokes.