A lot of hardcore fighting gamers will tell you that you have to have a stick to be any good. You can ignore those people. As part of any company's standard testing routine, you must be able to do anything in the game using any of the supported input methods (controller, fight stick, fight pad, etc.). Not only that, but there are tournament players who win using pads. The trials are definitely possible.
What I would recommend if you're having trouble, is looking up a full trial run on youtube for your character. Sometimes just seeing how the combo is supposed to look is what you need to complete it. On top of that, a good way to master an extended combo is to break it into small parts (like single links or cancels) and then slowly put the pieces together.
With charge characters, there's not much you can do to hide the fact that you are charging (for the most part, sliding input buffers allow you to mask charge somewhat).
However, this is part of the balance of the game, moves that require a charge such as this usually have quick recovery time.
In your specific example, Guile has the fastest recovery time in the game with his projectiles (outside of Seth).
Ryu (even though he has a great projectile) has some recovery time and you can punish him easier than you would Guile.
Speaking about Guile specifically, you can perform a Sonic Boom and retain the charge for the Flash Kick. If you hold the controller down and back, the charge counts for both down and back. If you perform the Sonic Boom like so:
Then you'll be able to perform the Sonic Boom while still retaining the charge for the Flash Kick. If someone jumps late enough, since you still have the joystick in the down position and retain the charge for the Flash Kick.
Note that joysticks with square gates make this much easier to perform than on pad (with a square gate joystick, you can move the stick along the bottom edge, as opposed to a pad where you have to roll your thumb across the D-pad or roll the thumbstick, which is round).
Best Answer
There are some ways to make your input easier, but not like SFxT.
Here are your options:
Aside from that I suggest you get a good controller or a fightstick. I personally prefer fightsticks with Senwa buttons. If you prefer only buttons there is also a controller called Hitbox that is basically a fightstick with only buttons. You can look up some hitbox Street Fighter tutorials like these ones: see shoryuken.com forums