Every car that I run on the layout uses Micro-Trains trucks, couplers and low-profile (small flanges) wheelsets. The trucks are used because they work the best on my layout, and because most of my couplers are truck mounted, so I need them to use the MT couplers. The couplers are used because I have found them to be the only couplers that work for delayed uncoupling. The low-profile wheelsets are used both for looks (they eliminate the "Mini-Lionel" look of the "pizza cutter" wheelsets), and because you need them to run the cars on the code 40 rail spurs. With the smaller flanges, the cars are more apt to derail, especially during certain switching moves. But I've found that adding weight to the cars mostly eliminates that problem for me.
I also install Micro-Train's restraining springs on one axle on each car. Initially, I did this to keep the trains running smoothly (eliminating the bouncing accordian effect, whether the caboose is connected or not), but I also found that the cars will stay put on the grades as if brakes were applied, which allows me much more flexibility when I am switching cars around. The combination of extra weight and restraining springs on the cars obviously makes them harder to pull up grade, which decreases the number of cars a single engine could pull around the layout. But this is hasn't been a problem, because the trains are normally short enough to begin with, and it's not a problem to double up engines when the train is long enough.
At this time, I do not expect to be adding Z couplers to any of the cars, except maybe the cabooses. I still have to figure out how I would want to convert the cars, and the trucks are easily removed for changing the couplers if I want to add them down the line anyway. I keep the couplers truck mounted for the most part, because they normally work better around the tight curves.