Having the same question a few years ago, I will give you my .02c worth. The CR and KX 500's are twin warriors of the 80's and 90's. Both are light and powerful. I have owned and ridden, modded and competed on as early as the CR480 and KX420. We built and modded both in about every way imaginable. There are some slight differences, but only slight. We found the CR doesn't have the life when modded, especially compression. There is an old piston rock issue that everyone knows. The soft steel cylinder requires boring and oversizing. The coolant capacity in the cylinder is only 29oz. They do get warm. All bad? Not at all. I just want to give you the honnest reply. There has never been a bigger love for a brutal dirt widow maker than the CR500. Part of the love was the era, "Ride Red". It dominated the world at the time. Was an excellent Moto bike. The CR500 ignition in it's OEM form is superior.
The KX500, Brutally powerful. Uncontested the #1 most powerful dirt bike ever made. It was developed ahead of it's time, "speaking engine". There is an extensive port diagram on cad describing the KX cylinder and it's technology. Common now, but revolutionary in it's time. It has a big cylinder, lots of cooling, Nikasil cylinder and KIPS exhaust valve. You can port, comp, and build that engine up and it will run flawlessly for years. Some old quotes of the day, "indestructible", could swallow a gallon of dirt and keep running. Their frame and suspension were far short of the CR. The KX shined as a desert racer and it's amazing engine. The power valve is huge. Every modern 2 stroke today has an exhaust power valve for all the obvious reasons. Smooth, fuel efficient, huge torque with the valve closed, then a smooth transition as it opens and get's on the pipe. I don't know of any modern 2 stroke engine without an exhaust power valve. The nikasil cylinder is also excellent modern technology. You can keep the OEM bore for life.
I chose the KX for the first big 2 stroke 500 build. "Service KX500 Monster" thread. I had a great time, learned a lot. It ran beautifully all year doing demo's etc without one hick-up. We have come a long way in 3 years. Primer, de-comp, etc. They are a viable option for big HP on a budget.