I shorten my workouts if time is an issue OR if I just simply don't like a particular move. Like you, it used to bother me to skip segments or do a premix, but I had an "ah-ha" moment.
Now that I exercise in the morning before work, I do not have a choice but to limit my exercise time. So, that means I always have to plan out my week. There are SO many combinations. It really depends on what you like.
If it's cardio that doesn't fit into my time frame, I simply skip the parts that I do not like or I do a premix. For strength training, it really depends on what type of split I'm doing for the week. Right now, I'm doing (Mon) Cathe's Fit Tower Total body but I skip the triceps exercises. Tues, I do the first 30 minutes of ICE Rock'm Sock'm and then the triceps muscle meltdown. Wed, Cathe S&S Total Body Giant Sets - lower body only. Doing lower body only allows me to do S&S Ramped Up Upper Body on Thurs. And Friday is fun cardio day.
I would start by planning out your week. The more you mix & match, the better you'll get at figuring out what you want to shorten, skip, etc.
Hope that helps!