If with raiden a pull jX, A,A,B (Juggle) A,A, X-RAY, I will do less damage than if I did jX, A,A,B, X-RAY
That is what damage scalling means. If you want high damage you must reset or if you want to finish it with a special/xraymove/ultra...etc and get maximum damage you should do a basic combo(aka as few hits as possible) + special
here is an example for sf4
After a certain number of hits all of the combos in Street Fighter IV start taking off less damage.
100% damage for first and second hits of a combo.
80% damage for third hit.
70% damage for fourth hit.
60% damage for fifth hit.
50% damage for sixth hit.
40% damage for seventh hit.
30% damage for eighth hit.
20% damage for ninth hit.
And each hit beyond the ninth drops the damage by an additional 10%.