I don't think you're seeing any design improvements at all. I think you've experienced a combination of bad luck and simply how things are for these items.
The two bad motors must purely be down to a batch of out of spec motors that you have probably had two of. I've never had any issues with any of the motors in the array of power units I have. And I've never had problems with the LEDs....and knowing how reliable solid state components can be nowadays, I'm somewhat puzzled as to why you've had an issue with one as well as two motors. You say you've only used the standard TGauge controllers. Have you used an external power supply, or only batteries?? If an external supply, then I'd check that out as it may be a common denominator if the voltage is possibly too high!
Regarding the reluctance to run smoothly first thing, this is something I've recently been discussing with martink in a PM exchange. We both have exactly the same experience with getting trains running at exhibitions. We've both found we need to run the power units on their own on full power for a few minutes to warm them up before adding wagons/carriages and gradually slowing them down to realistic speeds. We've both also had exactly the same issue with having to get a good order for coaches on the HSTs to prevent derailments, etc. I have a 3-car class 180 set where I have the two power cars marked...one runs at the front and one at the back. Run them the other way round and the carriage between them has a tendency to derail on tight corners. And we both find that towards the end of a running day, we need to speed the trains up a bit to ensure smooth running as wheels and track start to gum up a bit. All perfectly normal I'm afraid...and part of the fun of exhibiting a layout!
With respect to Graham's comments about differing running performances, I have had variance in performance as well. I put this fairly and sqarely down to differences in build tolerances causing differing running friction levels.....again part of what I would expect. I run in all my power units before I use them.....about a days worth of running at a smart pace, followed by a few hours at a much slower speed. If I get a stall, I run longer to free everything up more. And after this, they still need the running in at the start of the day.
Having said all that.....I'm looking forward to some much improved couplings I can use on longer consists like the HST. I had issues with derailing caused by the couplings not aligning properly and the springs holding the coupling too rigid. Removing the springs makes them run much better....but they're then a bugger to couple up! I did once try and use the fixed couplings....but you end up with a "snake" that's too hard to handle!!