I think some people are having adjustment problems. In FNR3 the upper cut started with what is now a Body shot (same with the hooks), so if you don't execute quick enough you throw the wrong punch. But that's not a flaw in the control scheme, the flaw was the one that you got used to and now it's fixed. Just need to adjust, that's all.
As for throwing the combos more consistantly, one point of advice. Slow down, instead of trying to move the sticks as fast as you can, relax and pick your spots. Keep in mind that the left/right hook is for Clubber Lang from rocky, unless your opponent is badly hurt, that combo is not thrown much in boxing. Maybe as part of a flurry, but not as a 1-2, try the jab/right or the straight/left combosand if they land then jump on the left/right. This is more effective for me, but everyone has their thing. But as far as boxing fundamentals, it's good science.