I can't say I'm a professional (or even well versed) SF4 player, so pardon any terminology discrepancies I make.
Though I've had a copy of SSF4 lying around for quite a while, I've gotten into it only recently and came across an issue that has always bugged me in fighting games.
While some characters (such as Ryu) have very precise means of performing special moves, others (such as Guile) require charging directional input in order to pull off a special move. I find that this charge really gives away your intentions (unless you pull off the move during some insane combo. That's not what I'm talking about) and makes it difficult to react with a special move quickly.
When I'm playing as Ryu, my opponent has no way of knowing that I'm about to dish out a Hadoken, and if he happens to jump over me, I can counter with a Shoryuken without too much preparation.
However, when I'm playing as Guile and I want to pull off a sonic boom, then I either have to start backing away, or crouch back to hold my position, both rather obvious giveaways. Also, there's no quick way to react with a Flash Kick when someone is jumping at you.
Again, Guile is just an example, and I have these issues with most charge based moves. Is there a better way to use such moves that I'm missing, or do you simply have to use characters with such moves in a different manner when playing?