I have a hell of a time finding pants that fit. If the waist fits, the butt and thighs are way tight. If the butt and thighs are big enough, the waist is at least 2" too big.
The pants I almost always wear are Vertx tactical pants, but unfortunately they have now changed the cut to make them much more slim-fitting, and I can't wear the new ones at all.
The old ones are great. They have a little elastic gather at the waist that is designed to allow for an inside the waistband holster, but has the effect of allowing a little more hip room without the waist being overly big. They also have a gusseted crotch, articulated knees and a rise that is not too long, which allow for great mobility -- you can squat without the pants binding or having to hike up the legs. And the cargo pockets are the best ever. They are recessed into the legs, so they don't stick out as obviously as "cargo" or "tactical" pants, but still hold a lot if you need them too. The pocket flaps are stitched down and without velco so you can get in and out of them easily with one hand and silently, but stuff doesn't fall out. There is also a concealed zipper pocket inside one of the regular front pockets that's great if you are carrying some loose change or other small object you want to make sure won't fall out when you sit down.
I wear these pretty much all the time (they are perfectly acceptable at my job), so I train in them when I do sets of various exercises throughout the day in my office during breaks.
There are now lots of pants that use stretch fabrics that allow for good mobility, but every one I have tried is still cut uncomfortably tight for me.
However, given a choice, such as when I train at home, I definitely prefer to train in shorts.